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Proteins
14:483-498
(1992)
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PubMed id:
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Modeling the anti-CEA antibody combining site by homology and conformational search.
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M.T.Mas,
K.C.Smith,
D.L.Yarmush,
K.Aisaka,
R.M.Fine.
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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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Literature references that cite this PDB file's key reference
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PubMed id
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PDB code:
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M.K.Fenwick,
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Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain.
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A complex fruit-specific type-2 ribosome-inactivating protein from elderberry (Sambucus nigra) is correctly processed and assembled in transgenic tobacco plants.
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Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
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PDB code:
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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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Links
