Related Experiment Video
Updated: Jul 13, 2026
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
Published on: October 13, 2022
Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis
Johnson Agniswamy1, Bin Fang, Irene T Weber
1Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30302, USA.
Abstract:
Many protein substrates of caspases are cleaved at noncanonical sites in comparison to the recognition motifs reported for the three caspase subgroups. To provide insight into the specificity and aid in the design of drugs to control cell death, crystal structures of caspase-7 were determined in complexes with six peptide analogs (Ac-DMQD-Cho, Ac-DQMD-Cho, Ac-DNLD-Cho, Ac-IEPD-Cho, Ac-ESMD-Cho, Ac-WEHD-Cho) that span the major recognition motifs of the three subgroups. The crystal structures show that the S2 pocket of caspase-7 can accommodate diverse residues. Glu is not required at the P3 position because Ac-DMQD-Cho, Ac-DQMD-Cho and Ac-DNLD-Cho with varied P3 residues are almost as potent as the canonical Ac-DEVD-Cho. P4 Asp was present in the better inhibitors of caspase-7. However, the S4 pocket of executioner caspase-7 has alternate regions for binding of small branched aliphatic or polar residues similar to those of initiator caspase-8. The observed plasticity of the caspase subsites agrees very well with the reported cleavage of many proteins at noncanonical sites. The results imply that factors other than the P4-P1 sequence, such as exosites, contribute to the in vivo substrate specificity of caspases. The novel peptide binding site identified on the molecular surface of the current structures is suggested to be an exosite of caspase-7. These results should be considered in the design of selective small molecule inhibitors of this pharmacologically important protease.
Insights
Caspase-7 crystal structures reveal flexible binding sites, accommodating diverse peptide inhibitors beyond canonical motifs. This plasticity explains noncanonical protein cleavage and guides the design of targeted cell death drugs.
Area of Science:
- Biochemistry
- Structural Biology
- Drug Discovery
Background:
- Caspases are key proteases regulating apoptosis, but their substrate specificity is not fully understood.
- Many protein substrates are cleaved at noncanonical sites, deviating from known caspase recognition motifs.
Purpose of the Study:
- To elucidate caspase-7 specificity by determining crystal structures with various peptide inhibitors.
- To provide insights for designing selective drugs targeting caspases and controlling cell death.
Main Methods:
- Determined crystal structures of caspase-7 in complex with six peptide analogs.
- Analyzed peptide binding within caspase-7's active site, focusing on subsites S2 and S4.
Main Results:
- Caspase-7's S2 pocket accommodates diverse residues, and Glu is not essential at P3.
- The S4 pocket shows plasticity, binding varied residues similar to caspase-8.
- A novel peptide binding site, potentially an exosite, was identified on the caspase-7 surface.
Conclusions:
- Caspase-7 exhibits significant substrate flexibility, explaining noncanonical cleavage events.
- Factors beyond the P4-P1 sequence, like exosites, are crucial for in vivo substrate specificity.
- Findings are critical for developing selective small molecule caspase inhibitors.
Related Concept Videos
01:24Caspases
01:17The Extrinsic Apoptotic Pathway
01:31The Intrinsic Apoptotic Pathway