ArticleFrontiers in genetics2019
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Data Processing and Analysis in Positional Proteomics.Proteomics · 2025Review
- Repercussions of the Calpain Cleavage-Related Missense Mutations in the Cytosolic Domains of Human Integrin-β Subunits on the Calpain-Integrin Signaling Axis.International journal of molecular sciences · 2025Article
- Caspase 3 and caspase 7 promote cytoprotective autophagy and the DNA damage response during non-lethal stress conditions in human breast cancer cells.PLoS biology · 2025Article
- Article
- Calpain-1 weakens the nuclear envelope and promotes the release of neutrophil extracellular traps.Cell communication and signaling : CCS · 2024Article
- Gene knockout of RNA binding motif 5 in the brain alters RIMS2 protein homeostasis in the cerebellum and Hippocampus and exacerbates behavioral deficits after a TBI in mice.Experimental neurology · 2024Article
- DiCleave: a deep learning model for predicting human Dicer cleavage sites.BMC bioinformatics · 2024Article
- Effects of truncations in the N- and C-terminal domains of filensin on filament formation with phakinin in cell-free conditions and cultured cells.FEBS open bio · 2023Article
- Calpain Regulation and Dysregulation-Its Effects on the Intercalated Disk.International journal of molecular sciences · 2023Review
- N-Terminomic Changes in Neurons During Excitotoxicity Reveal Proteolytic Events Associated With Synaptic Dysfunctions and Potential Targets for Neuroprotection.Molecular & cellular proteomics : MCP · 2023Article
- Neuronal activity regulates Matrin 3 abundance and function in a calcium-dependent manner through calpain-mediated cleavage and calmodulin binding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structure-Guided Prediction of the Functional Impact of DCLK1 Mutations on Tumorigenesis.Biomedicines · 2023Review
- RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication.Nucleic acids research · 2023Article
- Membrane-anchored calpains - hidden regulators of growth and development beyond plants?Frontiers in plant science · 2023Article
- Olfactory marker protein is unlikely to be cleaved by calpain 5.Molecular brain · 2022Article
- Reg-1α, a New Substrate of Calpain-2 Depending on Its Glycosylation Status.International journal of molecular sciences · 2022Article
- Recent Advances Regarding the Molecular Mechanisms of Triterpenic Acids: A Review (Part I).International journal of molecular sciences · 2022Review
- Calpain cleavage of Junctophilin-2 generates a spectrum of calcium-dependent cleavage products and DNA-rich NTScientific reports · 2022Article
- Isolation of Platelet-Derived Exosomes from Human Platelet-Rich Plasma: Biochemical and Morphological Characterization.International journal of molecular sciences · 2022Article
- Machine Learning Approaches for Metalloproteins.Molecules (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As a widespread post-translational modification of proteins, calpain-mediated cleavage regulates a broad range of cellular processes, including proliferation, differentiation, cytoskeletal reorganization, and apoptosis. The identification of proteins that undergo calpain cleavage in a site-specific manner is the necessary foundation for understanding the exact molecular mechanisms and regulatory roles of calpain-mediated cleavage. In contrast with time-consuming and labor-intensive experimental methods, computational approaches for detecting calpain cleavage sites have attracted wide attention due to their efficiency and convenience. In this study, we established a novel computational tool named DeepCalpain (http://deepcalpain.cancerbio.info/) for predicting the potential calpain cleavage sites by adopting deep neural network and the particle swarm optimization algorithm. Through critical evaluation and comparison, DeepCalpain exhibited superior performance against other existing tools. Meanwhile, we found that protein interactions could enrich the calpain-substrate regulatory relationship. Since calpain-mediated cleavage was critical for cancer development and progression, we comprehensively analyzed the calpain cleavage associated mutations across 11 cancers with the help of DeepCalpain, which demonstrated that the calpain-mediated cleavage events were affected by mutations and heavily implicated in the regulation of cancer cells. These prediction and analysis results might provide helpful information to reveal the regulatory mechanism of calpain cleavage in biological pathways and different cancer types, which might open new avenues for the diagnosis and treatment of cancers.
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