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PDBsum entry 1aag
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Immunoglobulin
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PDB id
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1aag
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References listed in PDB file
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Key reference
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Title
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Modeling the anti-Cea antibody combining site by homology and conformational search.
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Authors
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M.T.Mas,
K.C.Smith,
D.L.Yarmush,
K.Aisaka,
R.M.Fine.
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Ref.
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Proteins, 1992,
14,
483-498.
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PubMed id
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Abstract
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A model for an antibody specific for the carcinoembryonic antigen (CEA) has been
constructed using a method which combines the concept of canonical structures
with conformational search. A conformational search technique is introduced
which couples random generation of backbone loop conformations to a simulated
annealing method for assigning side chain conformations. This technique was used
both to verify conformations selected from the set of known canonical structures
and to explore conformations available to the H3 loop in CEA ab initio.
Canonical structures are not available for H3 due to its variability in length,
sequence, and observed conformation in known antibody structures. Analysis of
the results of conformational search resulted in three equally probable
conformations for H3 loop in CEA. Force field energies, solvation free energies,
exposure of charged residues and burial of hydrophobic residues, and packing of
hydrophobic residues at the base of the loop were used as selection criteria.
The existence of three equally plausible structures may reflect the high degree
of flexibility expected for an exposed loop of this length. The nature of the
combining site and features which could be important to interaction with antigen
are discussed.
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Secondary reference #1
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Title
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Site directed mutagenesis of the anti-Cea antibody combining site
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Authors
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S.Z.Hu,
K.Aisaka,
A.D.Riggs,
M.T.Mas.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #2
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Title
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Monoclonal antibodies for carcinoembryonic antigen and related antigens as a model system: a systematic approach for the determination of epitope specificities of monoclonal antibodies.
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Authors
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C.Wagener,
Y.H.Yang,
F.G.Crawford,
J.E.Shively.
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Ref.
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J Immunol, 1983,
130,
2308-2315.
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PubMed id
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