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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Introduction
The word “Caspase” stands for “Cysteine dependant aspartate directed protease” and represents a whole family of proteins (12). Proteins of the caspase family are essential enzymes involved in inflammation, necrosis and apoptosis process.
General fonction and mechanism
During the programmed cell death process, an apoptotic signal activates initiator caspases which gather in large protein complexes where they autoactivate. Then, they are able to activate in turn other capsases, called executioner caspases. Once activated, these executioner caspases will activate effectors which will finally lead to the cell apoptosis.
Caspase 7 is one of these executioner caspase.
Structure of the Caspase-7
The structure of the caspase-7 results directly from the maturation of the procaspase-7 zymogen by an initiator caspase. (cf. wiki)
Structure of the Procaspase-7
In the cytoplasm, caspases are not already, constitutively present in their active form. They exist as free cytoplasmic inactive precursors called procaspases.
Procaspase-7 is a homodimeric globular-303 amino-acids long polypeptide. This protein contains , representing two catalytic units. Each of these monomers is composed by a central 6-stranded β-sheet and 5 α-helices, forming a and a subunit, linked by a . The homodimerization is performed thanks to hydrophobic interactions between the 6 β-strands of each monomer. This homodimer is organized in a “open α/β barrel fold”.
Four loops (L1 to L4), located at the two opposite ends of the β–sheet, emanate from each homodimer and define the shape of the catalytic groove of each monomer.
links the two the large and small subunit of each procaspase-7 monomer. In the procaspase-7, this loop is in a “closed” conformation that precludes any possibility of substrate or inhibitor binding to the yet incomplete active site. Thus, in this considered conformation, the enzyme is yet inactive. This highly flexible loop contains two cleavage sites (Asp198 - Asp207) which are essential to the maturation of the Procaspase-7 (cf MATURATION). It also contains an essential residue needed for the catalytic activity of the Caspase-7 :
is a part of the large subunit, while and belong to the small subunit of each monomer. These three loops will also participate in the formation of the catalytic site.
The 23 last amino acids of the N-ter extremity of procaspase-7 define a “prodomain”. This prodomain is apparently implicated in an inhibitory mechanism that maintains the procaspase (or caspase) catalytically inactive until it is cleaved. The mechanism by which the prodomain could inhibit caspase-7 enzymatic activity is still unclear.
Maturation
In the active site of a caspase, a specific cystein residue is essential for the proteolytic activity of the enzyme.
Caspases are structurally designed to recognize a very specific sequence in their substrate and are able to cleave this protein after an Asp residue.
Procaspase-7 maturation is triggered by an initiator caspase (e.g. Caspase-9).This protein is able to cleave the interdomain of each monomer of the Procaspase-7. An entire sequence, from (mieux dit ? s’étalant de…) Asp198 to Ala207 is removed, thus separating the large and small subunits of each monomer.
Another cleavage can occur at the N-ter of the Procaspase-7 (Asp23), resulting in the release of the prodomain. However, it has been observed that this N-ter prodomain removal is not systematically necessary to obtain the caspase catalytic activity, while it is a warranty step for other proteases.
These modifications lead to the division of the L2 loop into two new loops : L2 and L2’. As a result, L2 becomes the C-terminal domain of the large subunit and L2’, (a.k.a “the critical loop”) constitutes the N-terminal extremity of the small subunit.
L2 changes its direction by 90°, while the L2’ loop remains folded and will only unfold once the substrate actually binds to the new formed operational catalytic groove. The main catalytic cysteine is harboured by this L2 loop and traverses the groove.
At the same time, a conformational change of L3 and L4 occur.
L3 forms the base of the catalytic groove.
L4 forms one side of the catalytic groove, rotates 60 ° and moves opposite of L3, further flattening the active site pocket. L1 constitutes the second side of this substrate-binding groove.
Finally, all the loops form a “loop-bundle”, giving rise to a recognizable substrate binding site. This loop-bundle is able to interact with the substrate in the matured, active caspase-7 form.
This substrate binding will then further induce a conformational switch of the caspase-7, leading to the hydrolysis of the substrate.
Structure of the free Caspase-7
Comparison and therapeutic interest
References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
