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Literature DB >> 20526345

Complementary positional proteomics for screening substrates of endo- and exoproteases.

Petra Van Damme¹, An Staes, Silvia Bronsoms, Kenny Helsens, Niklaas Colaert, Evy Timmerman, Francesc X Aviles, Joël Vandekerckhove, Kris Gevaert.

Abstract

We describe a positional proteomics approach to simultaneously analyze N- and C-terminal peptides and used it to screen for human protein substrates of granzyme B and carboxypeptidase A4 in human cell lysates. This approach allowed comprehensive proteome studies, and we report the identification of 965 database-annotated protein C termini, 334 neo-C termini resulting from granzyme B processing and 16 neo-C termini resulting from carboxypeptidase A4 processing.

Entities: Gene Species

Mesh：

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Year: 2010 PMID： 20526345 DOI： 10.1038/nmeth.1469

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

20 in total

1. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis.

Authors: Petra Van Damme; Lennart Martens; Jozef Van Damme; Koen Hugelier; An Staes; Joël Vandekerckhove; Kris Gevaert
Journal: Nat Methods Date: 2005-10 Impact factor: 28.547

2. Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs.

Authors: Petra Van Damme; Sebastian Maurer-Stroh; Kim Plasman; Joost Van Durme; Niklaas Colaert; Evy Timmerman; Pieter-Jan De Bock; Marc Goethals; Frederic Rousseau; Joost Schymkowitz; Joël Vandekerckhove; Kris Gevaert
Journal: Mol Cell Proteomics Date: 2008-10-03 Impact factor: 5.911

3. Improved visualization of protein consensus sequences by iceLogo.

Authors: Niklaas Colaert; Kenny Helsens; Lennart Martens; Joël Vandekerckhove; Kris Gevaert
Journal: Nat Methods Date: 2009-11 Impact factor: 28.547

4. Targeted analysis of protein termini.

Authors: Wilma Dormeyer; Shabaz Mohammed; Bas van Breukelen; Jeroen Krijgsveld; Albert J R Heck
Journal: J Proteome Res Date: 2007-10-10 Impact factor: 4.466

5. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins.

Authors: Kris Gevaert; Jozef Van Damme; Marc Goethals; Grégoire R Thomas; Bart Hoorelbeke; Hans Demol; Lennart Martens; Magda Puype; An Staes; Joël Vandekerckhove
Journal: Mol Cell Proteomics Date: 2002-11 Impact factor: 5.911

6. Carboxypeptidase A3 (CPA3): a novel gene highly induced by histone deacetylase inhibitors during differentiation of prostate epithelial cancer cells.

Authors: H Huang; C P Reed; J S Zhang; V Shridhar; L Wang; D I Smith
Journal: Cancer Res Date: 1999-06-15 Impact factor: 12.701

7. Expression and purification of recombinant human granzyme B from Pichia pastoris.

Authors: J Sun; C H Bird; M S Buzza; K E McKee; J C Whisstock; P I Bird
Journal: Biochem Biophys Res Commun Date: 1999-08-02 Impact factor: 3.575

8. Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin.

Authors: Irantzu Pallarès; Roman Bonet; Raquel García-Castellanos; Salvador Ventura; Francesc X Avilés; Josep Vendrell; F Xavier Gomis-Rüth
Journal: Proc Natl Acad Sci U S A Date: 2005-02-28 Impact factor: 11.205

9. A new method for C-terminal sequence analysis in the proteomic era.

Authors: Bart Samyn; Kjell Sergeant; Pedro Castanheira; Carlos Faro; Jozef Van Beeumen
Journal: Nat Methods Date: 2005-02-17 Impact factor: 28.547

10. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Authors: Shao-En Ong; Blagoy Blagoev; Irina Kratchmarova; Dan Bach Kristensen; Hanno Steen; Akhilesh Pandey; Matthias Mann
Journal: Mol Cell Proteomics Date: 2002-05 Impact factor: 5.911

32 in total

Review 1. Protease signalling: the cutting edge.

Authors: Boris Turk; Dušan Turk; Vito Turk
Journal: EMBO J Date: 2012-02-24 Impact factor: 11.598

2. Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion.

Authors: Geert P M Mommen; Bas van de Waterbeemd; Hugo D Meiring; Gideon Kersten; Albert J R Heck; Ad P J M de Jong
Journal: Mol Cell Proteomics Date: 2012-06-22 Impact factor: 5.911

Complementary positional proteomics for screening substrates of endo- and exoproteases.

1. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis.

2. Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs.

3. Improved visualization of protein consensus sequences by iceLogo.

4. Targeted analysis of protein termini.

5. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins.

6. Carboxypeptidase A3 (CPA3): a novel gene highly induced by histone deacetylase inhibitors during differentiation of prostate epithelial cancer cells.

7. Expression and purification of recombinant human granzyme B from Pichia pastoris.

8. Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin.

9. A new method for C-terminal sequence analysis in the proteomic era.

10. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Review 1. Protease signalling: the cutting edge.

2. Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion.

3. Alterations in RNA processing during immune-mediated programmed cell death.

Review 4. Proteolytic post-translational modification of proteins: proteomic tools and methodology.

5. Chemoenzymatic labeling of protein C-termini for positive selection of C-terminal peptides.

6. TopFIND, a knowledgebase linking protein termini with function.

7. Selecting protein N-terminal peptides by combined fractional diagonal chromatography.

8. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification.

9. Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome.

10. Granzyme M targets host cell hnRNP K that is essential for human cytomegalovirus replication.