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Related Concept Videos

Caspases01:24

Caspases

Caspase, a family of cysteine proteases, serve as effectors in apoptosis. The ced3 gene in C.elegans was first identified to be involved in apoptosis. This gene encodes the ced-3 caspase that is similar to the interleukin-1-beta converting enzyme or ICE in mammals. In addition to apoptosis, caspases also function in the inflammatory response. Inflammatory caspases are essential in activating pro-inflammatory cytokines that recruit immune cells and block the replication of pathogens inside cells.
Regulated Protein Degradation02:58

Regulated Protein Degradation

It is vital to regulate the activity of enzymatic as well as non-enzymatic proteins inside the cell. This can be achieved either through creating a balance between their rate of synthesis and degradation or regulating the intrinsic activity of the protein. Both these regulation mechanisms play an essential role in the normal functioning of cells.
Protein degradation plays two important roles in the cells. It helps to protect cells from misfolded or damaged proteins before they lead to a...
Regulated Protein Degradation02:58

Regulated Protein Degradation

It is vital to regulate the activity of enzymatic as well as non-enzymatic proteins inside the cell. This can be achieved either through creating a balance between their rate of synthesis and degradation or regulating the intrinsic activity of the protein. Both these regulation mechanisms play an essential role in the normal functioning of cells.
Protein degradation plays two important roles in the cells. It helps to protect cells from misfolded or damaged proteins before they lead to a...
The Intrinsic Apoptotic Pathway01:31

The Intrinsic Apoptotic Pathway

Internal cellular stress, such as cellular injury or hypoxia, triggers intrinsic apoptosis. The B-cell lymphoma 2 (Bcl-2) family of proteins are the primary regulators of the intrinsic apoptotic pathway. For example, during DNA damage, checkpoint proteins, such as Ataxia Telangiectasia Mutated (ATM protein) and Checkpoints Factor-2 (Chk2) proteins, are activated. These proteins phosphorylate p53 which further activates pro-apoptotic proteins, such as Bax, Bak, PUMA, and Noxa, and inhibits...
The Extrinsic Apoptotic Pathway01:17

The Extrinsic Apoptotic Pathway

The extrinsic apoptotic pathway is initiated when extracellular death-inducing signals, such as specific cytokines, activate the death receptors expressed on the cell surface. The immune cells involved in this pathway are natural killer cells (NK cells) and cytotoxic T-lymphocytes. NK cells are critical in innate immune response, while cytotoxic T-lymphocytes are associated with adaptive immune response. These cells recognize specific receptors expressed on the altered cells and activate...
Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA molecules by RNA...

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Related Experiment Video

Updated: Jun 18, 2026

Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry
05:29

Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry

Published on: March 24, 2023

A multi-factor model for caspase degradome prediction.

Lawrence J K Wee1, Joo Chuan Tong, Tin Wee Tan

  • 1Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. lawrence@bic.nus.edu.sg

BMC Genomics
|December 5, 2009
PubMed
Summary

This study introduces a new computational model to accurately predict caspase substrates by combining cleavage site prediction with structural factors like disorder and solvent exposure. This enhanced method significantly reduces false positives, aiding in the study of caspases in human health and disease.

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Last Updated: Jun 18, 2026

Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry
05:29

Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry

Published on: March 24, 2023

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

Lighting Up the Pathways to Caspase Activation Using Bimolecular Fluorescence Complementation
08:47

Lighting Up the Pathways to Caspase Activation Using Bimolecular Fluorescence Complementation

Published on: March 5, 2018

Area of Science:

  • Biochemistry
  • Proteomics
  • Computational Biology

Background:

  • Caspases are cysteine proteases crucial for apoptosis and inflammation.
  • Identifying caspase substrates (the caspase degradome) is vital for understanding human health and disease.
  • Existing computational methods for predicting caspase cleavage sites generate many false positives.

Purpose of the Study:

  • To develop an accurate computational method for predicting in vivo caspase substrates.
  • To improve upon existing cleavage site prediction tools by incorporating structural factors.
  • To reduce false positives in caspase substrate prediction.

Main Methods:

  • Developed a two-step prediction model combining sequence-based cleavage site prediction (using CASVM or GraBCas) with structural factors.
  • Incorporated analysis of disordered and solvent-exposed regions near cleavage sites.
  • Validated the model on an independent dataset of caspase substrates.

Main Results:

  • The enhanced model achieved higher positive predictive values compared to standalone prediction tools.
  • Reduced false positives by up to 13% (CASVM) and 53% (GraBCas) while retaining all true positives.
  • Identified several receptor tyrosine kinases (RTKs) as potential caspase targets, suggesting a role in apoptosis.

Conclusions:

  • Developed an accurate, multi-factor computational method for predicting in vivo caspase substrates.
  • The model enhances existing prediction tools and aids experimental efforts to define the caspase degradome.
  • Findings suggest RTKs are regulated by caspase cleavage, impacting cell death pathways.