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Apoptosis

, Volume 23, Issue 3–4, pp 194–200 | Cite as

Effect of phosphorylation and single nucleotide polymorphisms on caspase substrates processing

  • Sonu Kumar
  • Piotr Cieplak
Original Paper

Abstract

Posttranslational modifications that involve either reversible covalent modification of proteins or irreversible proteolysis are central to the regulation of key cellular mechanisms, including apoptosis, cell-cycle regulation and signal transduction. There is mounting evidence suggesting cross-talk between proteases and kinases. For instance: caspases, a class of proteases involved in programmed cell death—apoptosis, cleave a large set of various types of proteins. Simultaneously, kinases restrict caspase activity by phosphorylating their protein substrates in the vicinity of cleavage site. In addition, the caspase cleavage pattern in target proteins may be modified as a result of single nucleotide polymorphisms (SNPs) in the coding gene. This may either create a novel cleavage site, or increase/decrease the cleavage efficiency of a substrate. Such point mutations are often associated with the onset of disease. In this study, we predicted how phosphorylation and SNPs affect known human caspase proteolytic events collected in the CASBAH and Degrabase databases by applying Random Forest caspases’ substrates prediction method, as implemented in the CaspDB, and the molecular dynamics free energy simulations approach. Our analysis confirms several experimental observations. Phosphorylation could have both positive or negative regulatory effects depending on its position with respect to the caspase cleavage site. For instance, we demonstrate that phosphorylation at P1′ is the most detrimental for proteolytic efficiency of caspases. Phosphorylation at the P2 and P2′ positions also negatively affect the cleavage events. In addition, we uncovered SNPs in 11 caspase substrates capable of completely abolishing the cleavage site due to polymorphism at the P1 position. The findings presented here may be useful for determining the link between aberrant proteolysis and disease.

Keywords

Apoptosis Caspase substrates Phosphorylation SNPs Posttranslational modification of proteins Cross-talk between posttranslational modifications 

Abbreviations

SNP

Single nucleotide polymorphism

MM/GBSA

Molecular mechanics–generalized born surface area

Notes

Acknowledgements

This work has been supported by National Institute of Health Grant Number: R01GM098835 (PC). We thank Dr. Bram van Raam for valuable discussions and his corrections to the text.

Supplementary material

10495_2018_1442_MOESM1_ESM.png (162 kb)
Supplementary Fig. S1 Effects on cleavage probability score at particular positions due to phosphorylation. Distribution of the cleavage probability score differences between original and phosphorylated peptides. Y-axis represents the score difference whereas X-axis represents number of substrates having this score difference (PNG 162 KB)
10495_2018_1442_MOESM2_ESM.xlsx (161 kb)
Supplementary S1 File. List of caspase substrates having phosphorylation and SNPs including effects on proteolytic events. Excel sheets with name SNPs: shows list of substrates having SNPs in the vicnity of cleavage sites; Phosphorylations: shows list of all substrates having phosphorylations in the vicnity of the cleavage sites; Phos-P1 Prime, Phos-P2 Prime, Phos-P3 Prime, Phos-P2, Phos-P3, and Phos-P4: shows list of substrates having phosphorylation at respective sites (XLS 161 KB)
10495_2018_1442_MOESM3_ESM.docx (151 kb)
Table S1 List of experimentally verified known phosphorylation and SNP effects on caspase substrates cleavage efficiency. Top 14 substrates show inhibitory or increased or decreased cleavage efficiency due to phosphorylation. The last two entries (15 and 16) show the effect of SNP on cleavage efficiency. Phosphorylation and SNP are depicted using superscript and parentheses respectively (DOCX 151 KB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.SBP Medical Discovery InstituteLa JollaUSA
  2. 2.The Scripps Research InstituteLa JollaUSA

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