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PDBsum entry 1rog
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Histocompatibility antigen
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PDB id
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1rog
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References listed in PDB file
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Key reference
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Title
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Molecular dynamics simulation of mhc-Peptide complexes as a tool for predicting potential t cell epitopes.
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Authors
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D.Rognan,
L.Scapozza,
G.Folkers,
A.Daser.
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Ref.
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Biochemistry, 1994,
33,
11476-11485.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
90%.
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Abstract
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The class I major histocompatibility complex-encoded HLA-B*2705 protein was
simulated in complex with six different peptides exhibiting unexpected
structure-activity relationships. Various structural and dynamical properties of
the solvated protein-peptide complexes (atomic fluctuations, solvent-accessible
surface areas, hydrogen bonding pattern) were found to be in qualitative
agreement with the available binding data. Peptides that have been
experimentally shown to bind to the protein remained tightly anchored to the MHC
molecule, whereas nonbinders were significantly more weakly complexes to the
protein and progressively dissociate from it at their N- and C-terminal ends.
The molecular dynamics simulations emphasize the unexpectedly important role of
secondary anchors (positions 1 and 3) in influencing the MHC-bound conformation
of antigenic nonapeptides. Furthermore, it confirms that dominant anchor
residues cannot solely account for peptide binding to a class I MHC molecule.
The molecular dynamics method could be used as a complementary tool to T cell
epitope predictions from the primary sequences of proteins of immunological
interest. It is better suited to MHC proteins for which a crystal structure
already exists. Furthermore, it may facilitate the engineering of T cell
epitopes as well as the rational design of new MHC inhibitors designed to fit
optimally the peptide binding cleft.
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Secondary reference #1
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Title
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The three-Dimensional structure of hla-B27 at 2.1 a resolution suggests a general mechanism for tight peptide binding to mhc.
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Authors
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D.R.Madden,
J.C.Gorga,
J.L.Strominger,
D.C.Wiley.
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Ref.
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Cell, 1992,
70,
1035-1048.
[DOI no: ]
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PubMed id
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