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Contents |
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276 a.a.
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100 a.a.
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203 a.a.
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241 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Immune system/receptor
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Title:
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Structural and kinetic basis for heightened immunogenicity of t cell vaccines
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Structure:
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Hla class i histocompatibility antigen. Chain: a. Fragment: extracellular alpha-1, -2, -3, residues 25-300. Synonym: mhc, a-2 alpha chain precursor. Engineered: yes. Beta-2-microglobulin. Chain: b. Fragment: beta-2-microglobulin, residues 21-119. Synonym: hdcma22p, b2m.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cell: antigen presenting cell. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: refolded from inclusion bodies. Other_details: refolded from inclusion bodies from inclusion bodies. Synthetic: yes.
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Biol. unit:
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Pentamer (from PDB file)
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Resolution:
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Authors:
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J.-L.Chen,G.Stewart-Jones,G.Bossi,N.M.Lissin,L.Wooldridge,E.M.L.Choi, G.Held,P.R.Dunbar,R.M.Esnouf,M.Sami,J.M.Boultier,P.J.Rizkallah, C.Renner,A.Sewell,P.A.Van Der Merwe,B.K.Jackobsen,G.Griffiths, E.Y.Jones,V.Cerundolo
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Key ref:
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J.L.Chen
et al.
(2005).
Structural and kinetic basis for heightened immunogenicity of T cell vaccines.
J Exp Med,
201,
1243-1255.
PubMed id:
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Date:
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31-Mar-05
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Release date:
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23-May-05
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PROCHECK
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Headers
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References
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P04439
(1A03_HUMAN) -
HLA class I histocompatibility antigen, A alpha chain from Homo sapiens
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Seq:
Struc:
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365 a.a.
276 a.a.*
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P61769
(B2MG_HUMAN) -
Beta-2-microglobulin from Homo sapiens
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Seq:
Struc:
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119 a.a.
100 a.a.*
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A0A0B4J279
(TVA21_HUMAN) -
T cell receptor alpha variable 21 from Homo sapiens
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Seq:
Struc:
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112 a.a.
203 a.a.
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P01848
(TCA_HUMAN) -
T cell receptor alpha chain constant from Homo sapiens
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Seq:
Struc:
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140 a.a.
203 a.a.*
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J Exp Med
201:1243-1255
(2005)
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PubMed id:
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| |
|
Structural and kinetic basis for heightened immunogenicity of T cell vaccines.
|
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J.L.Chen,
G.Stewart-Jones,
G.Bossi,
N.M.Lissin,
L.Wooldridge,
E.M.Choi,
G.Held,
P.R.Dunbar,
R.M.Esnouf,
M.Sami,
J.M.Boulter,
P.Rizkallah,
C.Renner,
A.Sewell,
P.A.van der Merwe,
B.K.Jakobsen,
G.Griffiths,
E.Y.Jones,
V.Cerundolo.
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ABSTRACT
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Analogue peptides with enhanced binding affinity to major histocompatibility
class (MHC) I molecules are currently being used in cancer patients to elicit
stronger T cell responses. However, it remains unclear as to how alterations of
anchor residues may affect T cell receptor (TCR) recognition. We correlate
functional, thermodynamic, and structural parameters of TCR-peptide-MHC binding
and demonstrate the effect of anchor residue modifications of the human
histocompatibility leukocyte antigens (HLA)-A2 tumor epitope
NY-ESO-1(157-165)-SLLMWITQC on TCR recognition. The crystal structure of the
wild-type peptide complexed with a specific TCR shows that TCR binding centers
on two prominent, sequential, peptide sidechains, methionine-tryptophan.
Cysteine-to-valine substitution at peptide position 9, while optimizing peptide
binding to the MHC, repositions the peptide main chain and generates subtly
enhanced interactions between the analogue peptide and the TCR. Binding analyses
confirm tighter binding of the analogue peptide to HLA-A2 and improved soluble
TCR binding. Recognition of analogue peptide stimulates faster polarization of
lytic granules to the immunological synapse, reduces dependence on CD8 binding,
and induces greater numbers of cross-reactive cytotoxic T lymphocyte to
SLLMWITQC. These results provide important insights into heightened
immunogenicity of analogue peptides and highlight the importance of
incorporating structural data into the process of rational optimization of
superagonist peptides for clinical trials.
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
|
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Reference
|
|
|
|
|
|
J.R.James,
and
R.D.Vale
(2012).
Biophysical mechanism of T-cell receptor triggering in a reconstituted system.
|
| |
Nature,
487,
64-69.
|
|
|
|
|
|
|
J.M.Khan,
and
S.Ranganathan
(2011).
Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One.
|
| |
PLoS One,
6,
e17194.
|
|
|
|
|
|
|
K.M.Miles,
J.J.Miles,
F.Madura,
A.K.Sewell,
and
D.K.Cole
(2011).
Real time detection of peptide-MHC dissociation reveals that improvement of primary MHC-binding residues can have a minimal, or no, effect on stability.
|
| |
Mol Immunol,
48,
728-732.
|
|
|
|
|
|
|
D.K.Cole,
E.S.Edwards,
K.K.Wynn,
M.Clement,
J.J.Miles,
K.Ladell,
J.Ekeruche,
E.Gostick,
K.J.Adams,
A.Skowera,
M.Peakman,
L.Wooldridge,
D.A.Price,
and
A.K.Sewell
(2010).
Modification of MHC anchor residues generates heteroclitic peptides that alter TCR binding and T cell recognition.
|
| |
J Immunol,
185,
2600-2610.
|
|
|
|
|
|
|
G.I.van Boxel,
S.Holmes,
L.Fugger,
and
E.Y.Jones
(2010).
An alternative conformation of the T-cell receptor alpha constant region.
|
| |
J Mol Biol,
400,
828-837.
|
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|
PDB code:
|
|
|
|
|
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|
|
J.J.Miles,
A.M.Bulek,
D.K.Cole,
E.Gostick,
A.J.Schauenburg,
G.Dolton,
V.Venturi,
M.P.Davenport,
M.P.Tan,
S.R.Burrows,
L.Wooldridge,
D.A.Price,
P.J.Rizkallah,
and
A.K.Sewell
(2010).
Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection.
|
| |
PLoS Pathog,
6,
e1001198.
|
|
|
PDB code:
|
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|
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|
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L.F.Poulin,
M.Salio,
E.Griessinger,
F.Anjos-Afonso,
L.Craciun,
J.L.Chen,
A.M.Keller,
O.Joffre,
S.Zelenay,
E.Nye,
A.Le Moine,
F.Faure,
V.Donckier,
D.Sancho,
V.Cerundolo,
D.Bonnet,
and
C.Reis e Sousa
(2010).
Characterization of human DNGR-1+ BDCA3+ leukocytes as putative equivalents of mouse CD8alpha+ dendritic cells.
|
| |
J Exp Med,
207,
1261-1271.
|
|
|
|
|
|
|
M.Aleksic,
O.Dushek,
H.Zhang,
E.Shenderov,
J.L.Chen,
V.Cerundolo,
D.Coombs,
and
P.A.van der Merwe
(2010).
Dependence of T cell antigen recognition on T cell receptor-peptide MHC confinement time.
|
| |
Immunity,
32,
163-174.
|
|
|
|
|
|
|
V.Zoete,
M.B.Irving,
and
O.Michielin
(2010).
MM-GBSA binding free energy decomposition and T cell receptor engineering.
|
| |
J Mol Recognit,
23,
142-152.
|
|
|
|
|
|
|
A.L.Rothman
(2009).
T lymphocyte responses to heterologous secondary dengue virus infections.
|
| |
Ann N Y Acad Sci,
1171,
E36-E41.
|
|
|
|
|
|
|
D.K.Cole,
F.Yuan,
P.J.Rizkallah,
J.J.Miles,
E.Gostick,
D.A.Price,
G.F.Gao,
B.K.Jakobsen,
and
A.K.Sewell
(2009).
Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor.
|
| |
J Biol Chem,
284,
27281-27289.
|
|
|
PDB code:
|
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|
|
|
|
|
|
G.Stewart-Jones,
A.Wadle,
A.Hombach,
E.Shenderov,
G.Held,
E.Fischer,
S.Kleber,
F.Stenner-Liewen,
S.Bauer,
A.McMichael,
A.Knuth,
H.Abken,
A.A.Hombach,
V.Cerundolo,
E.Y.Jones,
and
C.Renner
(2009).
Rational development of high-affinity T-cell receptor-like antibodies.
|
| |
Proc Natl Acad Sci U S A,
106,
5784-5788.
|
|
|
PDB codes:
|
|
|
|
|
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|
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J.K.Archbold,
W.A.Macdonald,
S.Gras,
L.K.Ely,
J.J.Miles,
M.J.Bell,
R.M.Brennan,
T.Beddoe,
M.C.Wilce,
C.S.Clements,
A.W.Purcell,
J.McCluskey,
S.R.Burrows,
and
J.Rossjohn
(2009).
Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.
|
| |
J Exp Med,
206,
209-219.
|
|
|
PDB codes:
|
|
|
|
|
|
|
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M.Iero,
P.Filipazzi,
C.Castelli,
F.Belli,
R.Valdagni,
G.Parmiani,
R.Patuzzo,
M.Santinami,
and
L.Rivoltini
(2009).
Modified peptides in anti-cancer vaccines: are we eventually improving anti-tumour immunity?
|
| |
Cancer Immunol Immunother,
58,
1159-1167.
|
|
|
|
|
|
|
N.A.Bowerman,
T.S.Crofts,
L.Chlewicki,
P.Do,
B.M.Baker,
K.Christopher Garcia,
and
D.M.Kranz
(2009).
Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity.
|
| |
Mol Immunol,
46,
3000-3008.
|
|
|
|
|
|
|
V.Cerundolo,
J.D.Silk,
S.H.Masri,
and
M.Salio
(2009).
Harnessing invariant NKT cells in vaccination strategies.
|
| |
Nat Rev Immunol,
9,
28-38.
|
|
|
|
|
|
|
X.Shang,
L.Wang,
W.Niu,
G.Meng,
X.Fu,
B.Ni,
Z.Lin,
Z.Yang,
X.Chen,
and
Y.Wu
(2009).
Rational optimization of tumor epitopes using in silico analysis-assisted substitution of TCR contact residues.
|
| |
Eur J Immunol,
39,
2248-2258.
|
|
|
|
|
|
|
D.I.Godfrey,
J.Rossjohn,
and
J.McCluskey
(2008).
The fidelity, occasional promiscuity, and versatility of T cell receptor recognition.
|
| |
Immunity,
28,
304-314.
|
|
|
|
|
|
|
D.Y.Lin,
Y.Tanaka,
M.Iwasaki,
A.G.Gittis,
H.P.Su,
B.Mikami,
T.Okazaki,
T.Honjo,
N.Minato,
and
D.N.Garboczi
(2008).
The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors.
|
| |
Proc Natl Acad Sci U S A,
105,
3011-3016.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
E.J.Collins,
and
D.S.Riddle
(2008).
TCR-MHC docking orientation: natural selection, or thymic selection?
|
| |
Immunol Res,
41,
267-294.
|
|
|
|
|
|
|
J.Fourcade,
P.Kudela,
P.A.Andrade Filho,
B.Janjic,
S.R.Land,
C.Sander,
A.Krieg,
A.Donnenberg,
H.Shen,
J.M.Kirkwood,
and
H.M.Zarour
(2008).
Immunization with analog peptide in combination with CpG and montanide expands tumor antigen-specific CD8+ T cells in melanoma patients.
|
| |
J Immunother,
31,
781-791.
|
|
|
|
|
|
|
J.Garcia Casado,
J.Janda,
J.Wei,
L.Chapatte,
S.Colombetti,
P.Alves,
G.Ritter,
M.Ayyoub,
D.Valmori,
W.Chen,
and
F.Lévy
(2008).
Lentivector immunization induces tumor antigen-specific B and T cell responses in vivo.
|
| |
Eur J Immunol,
38,
1867-1876.
|
|
|
|
|
|
|
J.Ishizuka,
G.B.Stewart-Jones,
A.van der Merwe,
J.I.Bell,
A.J.McMichael,
and
E.Y.Jones
(2008).
The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain.
|
| |
Immunity,
28,
171-182.
|
|
|
PDB codes:
|
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|
|
|
|
|
|
K.M.Armstrong,
K.H.Piepenbrink,
and
B.M.Baker
(2008).
Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes.
|
| |
Biochem J,
415,
183-196.
|
|
|
|
|
|
|
L.Derré,
M.Bruyninx,
P.Baumgaertner,
M.Ferber,
D.Schmid,
A.Leimgruber,
V.Zoete,
P.Romero,
O.Michielin,
D.E.Speiser,
and
N.Rufer
(2008).
Distinct sets of alphabeta TCRs confer similar recognition of tumor antigen NY-ESO-1157-165 by interacting with its central Met/Trp residues.
|
| |
Proc Natl Acad Sci U S A,
105,
15010-15015.
|
|
|
|
|
|
|
N.S.Butler,
A.Theodossis,
A.I.Webb,
R.Nastovska,
S.H.Ramarathinam,
M.A.Dunstone,
J.Rossjohn,
A.W.Purcell,
and
S.Perlman
(2008).
Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant.
|
| |
PLoS Pathog,
4,
e1000186.
|
|
|
PDB codes:
|
|
|
|
|
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|
P.F.Robbins,
Y.F.Li,
M.El-Gamil,
Y.Zhao,
J.A.Wargo,
Z.Zheng,
H.Xu,
R.A.Morgan,
S.A.Feldman,
L.A.Johnson,
A.D.Bennett,
S.M.Dunn,
T.M.Mahon,
B.K.Jakobsen,
and
S.A.Rosenberg
(2008).
Single and dual amino acid substitutions in TCR CDRs can enhance antigen-specific T cell functions.
|
| |
J Immunol,
180,
6116-6131.
|
|
|
|
|
|
|
P.Johansen,
T.Storni,
L.Rettig,
Z.Qiu,
A.Der-Sarkissian,
K.A.Smith,
V.Manolova,
K.S.Lang,
G.Senti,
B.Müllhaupt,
T.Gerlach,
R.F.Speck,
A.Bot,
and
T.M.Kündig
(2008).
Antigen kinetics determines immune reactivity.
|
| |
Proc Natl Acad Sci U S A,
105,
5189-5194.
|
|
|
|
|
|
|
P.Marrack,
J.P.Scott-Browne,
S.Dai,
L.Gapin,
and
J.W.Kappler
(2008).
Evolutionarily conserved amino acids that control TCR-MHC interaction.
|
| |
Annu Rev Immunol,
26,
171-203.
|
|
|
|
|
|
|
C.Mazza,
and
B.Malissen
(2007).
What guides MHC-restricted TCR recognition?
|
| |
Semin Immunol,
19,
225-235.
|
|
|
|
|
|
|
C.Mazza,
N.Auphan-Anezin,
C.Gregoire,
A.Guimezanes,
C.Kellenberger,
A.Roussel,
A.Kearney,
P.A.van der Merwe,
A.M.Schmitt-Verhulst,
and
B.Malissen
(2007).
How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?
|
| |
EMBO J,
26,
1972-1983.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.McCarthy,
D.Shepherd,
S.Fleire,
V.S.Stronge,
M.Koch,
P.A.Illarionov,
G.Bossi,
M.Salio,
G.Denkberg,
F.Reddington,
A.Tarlton,
B.G.Reddy,
R.R.Schmidt,
Y.Reiter,
G.M.Griffiths,
P.A.van der Merwe,
G.S.Besra,
E.Y.Jones,
F.D.Batista,
and
V.Cerundolo
(2007).
The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation.
|
| |
J Exp Med,
204,
1131-1144.
|
|
|
|
|
|
|
F.E.Tynan,
H.H.Reid,
L.Kjer-Nielsen,
J.J.Miles,
M.C.Wilce,
L.Kostenko,
N.A.Borg,
N.A.Williamson,
T.Beddoe,
A.W.Purcell,
S.R.Burrows,
J.McCluskey,
and
J.Rossjohn
(2007).
A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule.
|
| |
Nat Immunol,
8,
268-276.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.M.Boulter,
N.Schmitz,
A.K.Sewell,
A.J.Godkin,
M.F.Bachmann,
and
A.M.Gallimore
(2007).
Potent T cell agonism mediated by a very rapid TCR/pMHC interaction.
|
| |
Eur J Immunol,
37,
798-806.
|
|
|
|
|
|
|
L.Deng,
R.J.Langley,
P.H.Brown,
G.Xu,
L.Teng,
Q.Wang,
M.I.Gonzales,
G.G.Callender,
M.I.Nishimura,
S.L.Topalian,
and
R.A.Mariuzza
(2007).
Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor.
|
| |
Nat Immunol,
8,
398-408.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Iero,
P.Squarcina,
P.Romero,
P.Guillaume,
E.Scarselli,
R.Cerino,
M.Carrabba,
O.Toutirais,
G.Parmiani,
and
L.Rivoltini
(2007).
Low TCR avidity and lack of tumor cell recognition in CD8(+) T cells primed with the CEA-analogue CAP1-6D peptide.
|
| |
Cancer Immunol Immunother,
56,
1979-1991.
|
|
|
|
|
|
|
M.Salio,
A.O.Speak,
D.Shepherd,
P.Polzella,
P.A.Illarionov,
N.Veerapen,
G.S.Besra,
F.M.Platt,
and
V.Cerundolo
(2007).
Modulation of human natural killer T cell ligands on TLR-mediated antigen-presenting cell activation.
|
| |
Proc Natl Acad Sci U S A,
104,
20490-20495.
|
|
|
|
|
|
|
P.J.Miller,
Y.Pazy,
B.Conti,
D.Riddle,
E.Appella,
and
E.J.Collins
(2007).
Single MHC mutation eliminates enthalpy associated with T cell receptor binding.
|
| |
J Mol Biol,
373,
315-327.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.Douat-Casassus,
N.Marchand-Geneste,
E.Diez,
C.Aznar,
P.Picard,
S.Geoffre,
A.Huet,
M.L.Bourguet-Kondracki,
N.Gervois,
F.Jotereau,
and
S.Quideau
(2006).
Covalent modification of a melanoma-derived antigenic peptide with a natural quinone methide. Preliminary chemical, molecular modelling and immunological evaluation studies.
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Mol Biosyst,
2,
240-249.
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C.S.Clements,
M.A.Dunstone,
W.A.Macdonald,
J.McCluskey,
and
J.Rossjohn
(2006).
Specificity on a knife-edge: the alphabeta T cell receptor.
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Curr Opin Struct Biol,
16,
787-795.
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G.Røder,
T.Blicher,
S.Justesen,
B.Johannesen,
O.Kristensen,
J.Kastrup,
S.Buus,
and
M.Gajhede
(2006).
Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype.
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| |
Acta Crystallogr D Biol Crystallogr,
62,
1300-1310.
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PDB codes:
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J.A.Guevara-Patiño,
M.E.Engelhorn,
M.J.Turk,
C.Liu,
F.Duan,
G.Rizzuto,
A.D.Cohen,
T.Merghoub,
J.D.Wolchok,
and
A.N.Houghton
(2006).
Optimization of a self antigen for presentation of multiple epitopes in cancer immunity.
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J Clin Invest,
116,
1382-1390.
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K.M.Zirlik,
D.Zahrieh,
D.Neuberg,
and
J.G.Gribben
(2006).
Cytotoxic T cells generated against heteroclitic peptides kill primary tumor cells independent of the binding affinity of the native tumor antigen peptide.
|
| |
Blood,
108,
3865-3870.
|
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|
|
L.Banci,
I.Bertini,
S.Cusack,
R.N.de Jong,
U.Heinemann,
E.Y.Jones,
F.Kozielski,
K.Maskos,
A.Messerschmidt,
R.Owens,
A.Perrakis,
A.Poterszman,
G.Schneider,
C.Siebold,
I.Silman,
T.Sixma,
G.Stewart-Jones,
J.L.Sussman,
J.C.Thierry,
and
D.Moras
(2006).
First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value.
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| |
Acta Crystallogr D Biol Crystallogr,
62,
1208-1217.
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|
|
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|
L.K.Ely,
T.Beddoe,
C.S.Clements,
J.M.Matthews,
A.W.Purcell,
L.Kjer-Nielsen,
J.McCluskey,
and
J.Rossjohn
(2006).
Disparate thermodynamics governing T cell receptor-MHC-I interactions implicate extrinsic factors in guiding MHC restriction.
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| |
Proc Natl Acad Sci U S A,
103,
6641-6646.
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M.G.Rudolph,
R.L.Stanfield,
and
I.A.Wilson
(2006).
How TCRs bind MHCs, peptides, and coreceptors.
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| |
Annu Rev Immunol,
24,
419-466.
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N.Auphan-Anezin,
C.Mazza,
A.Guimezanes,
G.A.Barrett-Wilt,
F.Montero-Julian,
A.Roussel,
D.F.Hunt,
B.Malissen,
and
A.M.Schmitt-Verhulst
(2006).
Distinct orientation of the alloreactive monoclonal CD8 T cell activation program by three different peptide/MHC complexes.
|
| |
Eur J Immunol,
36,
1856-1866.
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|
PDB codes:
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R.L.Rich,
and
D.G.Myszka
(2006).
Survey of the year 2005 commercial optical biosensor literature.
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J Mol Recognit,
19,
478-534.
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S.D.Gadola,
M.Koch,
J.Marles-Wright,
N.M.Lissin,
D.Shepherd,
G.Matulis,
K.Harlos,
P.M.Villiger,
D.I.Stuart,
B.K.Jakobsen,
V.Cerundolo,
and
E.Y.Jones
(2006).
Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.
|
| |
J Exp Med,
203,
699-710.
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PDB codes:
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S.M.Dunn,
P.J.Rizkallah,
E.Baston,
T.Mahon,
B.Cameron,
R.Moysey,
F.Gao,
M.Sami,
J.Boulter,
Y.Li,
and
B.K.Jakobsen
(2006).
Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide-MHC without increasing apparent cross-reactivity.
|
| |
Protein Sci,
15,
710-721.
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|
|
PDB codes:
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Z.Tabi,
and
S.Man
(2006).
Challenges for cancer vaccine development.
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| |
Adv Drug Deliv Rev,
58,
902-915.
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B.Seliger
(2005).
Strategies of tumor immune evasion.
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BioDrugs,
19,
347-354.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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| |
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