Structure analysis and homology modeling of carcinoembryonic antigen
Carcinoembryonic antigen (CEA) is a glycosylated cell surface protein.
It has seven domains in the extracellular part. All these domains have typical
immunoglobulin fold. We use this example to learn how to compare protein
structures and how to do knowledge-based homology modeling.
Exercises:
- Search Swiss-Prot with query ID "CEAM5_HUMAN", find out the
sequence features of this molecule, use dotmatcher to draw a dotplot to
show the repeated domains of this molecule.
- Search Swiss-Prot with query text "human carcinoembryonic antigen",
find out different CEA members (CEAM1, CEAM3, CEAM5, CEAM6, CEAM7 and
CEAM8), compare the difference of these sub types.
- Retrieve the N-terminal domain of the above CEA members, make sequence
alignment and construct a phylogeny tree.
- Make multiple sequence alignment among the N-terminal domain of CEAM5_HUMAN
and the first domain of CD2 and CD4 as well as the variable domain of
the light chain of immunoglobulin (7FAB)
- Download the crystal structure of CEAM5 (1QSQ) and IgG (7FAB) from PDB,
use Swiss PDBViewer to compare the stricture features of these two molecules
Web resources:
- HPA
- CEACAM5 expression profiles at Human Protein Atlas
- AAAAA - AHo's Amazing
Atlas of Antibody Anatomy (Switzerland)
- AAIR
- Antibody Antigen Information Resource
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| 16 July 2008, J Luo, CBI, PKU, Beijing, China