Protein Modeling/Apoptosis

The 2012 topic of Protein Modeling deals with cell apoptosis. The pre-build model is of caspase-3.

See the CBM webpage for more details.

Caspase-3
Caspase-3 is the pre-build model for 2012, based on file 1I3O.pdb.

Caspase-3 is a cysteine-aspartic acid protease, known as an "executioner" protein because of the direct role it plays in dismantling other cell proteins during apoptosis. It is inhibited by XIAP, and it acts upon PARP, among other proteins.

Its active site contains a cysteine which directly attacks the substrate, cleaving the target protein at the amino side of an aspartic acid residue; hence the name "cysteine-aspartic acid protease".

Diablo
Diablo is the onsite model for Invitationals.

The Diablo homolog is an inhibitor of XIAP.

XIAP
XIAP is the onsite model for regionals, also based on file 1I3O.pdb.

XIAP is the X-linked Inhibitor of Apoptosis Protein, which inhibits apoptosis by binding to Caspase-3 (and other caspases) to prevent them from cleaving their substrates. It is called "X-linked" because the gene responsible for it is found on the X-chromosome.

XIAP is a competitive inhibitor (for caspase-3, at least; it has other inhibition mechanisms for other proteins), in that it binds directly to the active site of caspase-3, blocking the binding of its usual substrates.

Its BIR2 domain (the part that binds directly to caspase-3) contains a zinc finger in which one histidine and three cysteines coordinate a zinc ion.

PARP
PARP is the onsite model for states.

MHC
MHC is the onsite model for nationals.

Apoptosis
Apoptosis is the programmed death of a cell. It is triggered by signals either from mitochondria (i.e., the release of cytochrome c) or extrinsic signals caused by exposure to radiation, etc. In the process of apoptosis, structural and DNA-repair proteins are broken down.