N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatBPetra Van Damme
Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie, Ghent University, B 9000 Ghent, Belgium
Proc Natl Acad Sci U S A 109:12449-54. 2012
....
Protein alpha-N-acetylation studied by N-terminomicsPetra Van Damme
Department of Medical Protein Research, VIB, Ghent, Belgium
FEBS J 278:3822-34. 2011
..In this review, we report on such emerging technologies as well as on breakthroughs in our understanding of protein N-terminal biology...
- The substrate specificity profile of human granzyme A
Petra Van Damme
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Ghent, Belgium
Biol Chem 391:983-97. 2010
..Further substrate characterization was used to delineate physical properties in the substrate specificity profiles, which further highlights important aspects in protease/substrate biology...
- Probing the efficiency of proteolytic events by positional proteomics
Kim Plasman
Department of Medical Protein Research, VIB, Ghent, Belgium
Mol Cell Proteomics 10:M110.003301. 2011
..Several of our proteomics results were further confirmed by substrate immunoblotting and by using peptide substrates incubated with human granzyme B...
- MS-driven protease substrate degradomics
Francis Impens
Department of Medical Protein Research, VIB, Ghent, Belgium
Proteomics 10:1284-96. 2010
..The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS-driven protease substrate degradome studies...
- Selecting protein N-terminal peptides by combined fractional diagonal chromatography
An Staes
Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie VIB, Ghent, Belgium
Nat Protoc 6:1130-41. 2011
..Completion of the N-terminal COFRADIC procedure takes ~5 d...
- NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation
Petra Van Damme
Department of Medical Protein Research, Ghent University, Ghent, Belgium
PLoS Genet 7:e1002169. 2011
..With the characterization of NatF, the co-translational N-Ac machinery appears complete since all the major substrate groups in eukaryotes are accounted for...
A la carte proteomics with an emphasis on gel-free techniquesKris Gevaert
Department of Medical Protein Research, VIB, Ghent, Belgium
Proteomics 7:2698-718. 2007
..Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed...
- Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis
Petra Van Damme
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Belgium
Nat Methods 2:771-7. 2005
..The spliceosome complex appeared a preferred target, as 14 of its members were processed. Differential isotopic labeling further revealed specific release of nucleosomal components from apoptotic nuclei...
- Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of N(alpha)-acetyltransferases and point to hNaa10p as the post-translational actin N(alpha)-acetyltransferase
Petra Van Damme
Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
Mol Cell Proteomics 10:M110.004580. 2011
..Thus, complex formation of NatA might alter the substrate specificity profile as compared with its isolated catalytic subunits, and, furthermore, NatA or hNaa10p may function as a post-translational actin N(α)-acetyltransferase...
- Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation
Kenny Helsens
Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
J Proteome Res 10:3578-89. 2011
..Finally, we also observed an unexpected high number of N(α)-acetylated peptides that could not be related to TIS and therefore suggest events of post-translational N(α)-acetylation...
- Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses
Kris Gevaert
Department of Medical Protein Research, VIB, Ghent, Belgium
FEBS J 274:6277-89. 2007
..Additionally, we discuss an activity-based proteome study in which purine-binding proteins were profiled by diagonal chromatography...
- Complementary positional proteomics for screening substrates of endo- and exoproteases
Petra Van Damme
Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie, Ghent, Belgium
Nat Methods 7:512-5. 2010
....
- Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs
Petra Van Damme
Department of Medical Protein Research, Flanders Institute for Biotechnology VIB, Ghent, Belgium
Mol Cell Proteomics 8:258-72. 2009
....
- Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)
An Staes
Department of Medical Protein Research, VIB, Ghent, Belgium
Proteomics 8:1362-70. 2008
..We further show that now close to 95% of all COFRADIC-sorted peptides are alpha-amino-acetylated and, using the same amount of starting material, our novel procedure leads to an increased number of protein identifications...
- The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
Niklaas Colaert
Department of Medical Protein Research, VIB, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
Nucleic Acids Res 41:D333-7. 2013
..Across substrates, substrate orthologs and conserved sequence stretches can also be shown, with iceLogo visualization provided for the latter...
- Caspase-14 is required for filaggrin degradation to natural moisturizing factors in the skin
Esther Hoste
Molecular Signaling and Cell Death Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
J Invest Dermatol 131:2233-41. 2011
..Taken together, we identified caspase-14 as a crucial protease in FLG catabolism...
- Stable isotopic labeling in proteomics
Kris Gevaert
Department of Medical Protein Research, VIB, Ghent University, Ghent, Belgium
Proteomics 8:4873-85. 2008
..In this review article, commonly used isotope labeling strategies are described, both for quantitative differential protein profiling and for targeted analysis of protein modifications...
- Caspase substrates: easily caught in deep waters?
Dieter Demon
Department for Molecular Biomedical Research, VIB, B 9052 Ghent, Belgium
Trends Biotechnol 27:680-8. 2009
..Here, we critically review recently published procedures used to generate a proteome-wide view of caspase substrates...
- Proteome-wide Identification of HtrA2/Omi Substrates
Lieselotte Vande Walle
Department of Molecular Biomedical Research, VIB, 9052, Ghent, Belgium
J Proteome Res 6:1006-15. 2007
..Our results suggest that HtrA2/Omi has a rather narrow cleavage site preference and that cytoskeletal proteins are prime targets of this protease...
- Protein processing and other modifications analyzed by diagonal peptide chromatography
Kris Gevaert
Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
Biochim Biophys Acta 1764:1801-10. 2006
..Additional modifications that can be analyzed include phosphorylation and N-glycosylation. The potential of COFRADIC for isolating peptides holding such modified amino acids are discussed here...
- Protein processing characterized by a gel-free proteomics approach
Petra Van Damme
Ghent University, Ghent, Belgium
Methods Mol Biol 484:245-62. 2008
..As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research...
- Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?
Kris Gevaert
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
Anal Biochem 345:18-29. 2005
..We were able to identify an unexpectedly high number of intracellular proteins next to known biomarkers...
- A review of COFRADIC techniques targeting protein N-terminal acetylation
Petra Van Damme
Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
BMC Proc 3:S6. 2009
....
- N-terminal acetylation and other functions of Nα-acetyltransferases
Jolien Hollebeke
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, A Baertsoenkaai 3, B 9000 Ghent, Belgium
Biol Chem 393:291-8. 2012
..This minireview tries to summarize the recent progress made in understanding the functionality of N-terminal protein acetylation and also focuses on noncanonical functions of the NATs subunits...
- T-cell receptor-induced JNK activation requires proteolytic inactivation of CYLD by MALT1
Jens Staal
Department of Molecular Biomedical Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Zwijnaarde, Ghent, Belgium
EMBO J 30:1742-52. 2011
..These results indicate a novel role for MALT1 proteolytic activity in TCR-induced JNK activation and reveal CYLD cleavage as the underlying mechanism...
- Disentanglement of protease substrate repertoires
Petra Van Damme
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology VIB, B 9000 Ghent, Belgium
Biol Chem 389:371-81. 2008
..We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications...
- In-gel N-acetylation for the quantification of the degree of protein in vivo N-terminal acetylation
Petra Van Damme
Department of Medical Protein Research, VIB, Ghent, Belgium
Methods Mol Biol 981:115-26. 2013
....
- Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike
Magdalena Wejda
Department for Molecular Biomedical Research, Flanders Institute for Biotechnology VIB, Ghent University, B 9052 Ghent Zwijnaarde, Belgium
J Biol Chem 287:33983-95. 2012
....
- The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile
Lennart Martens
Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
Proteomics 5:3193-204. 2005
....
- Contemporary positional proteomics strategies to study protein processing
Kim Plasman
Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
Curr Opin Chem Biol 17:66-72. 2013
..Since proteases create novel termini in their substrates, positional proteomics is ideally suited for protease degradomics studies. We here review recent developments in the field of positional proteomics applied to protease research...
- Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii
Dirk Halet
Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium
FEMS Microbiol Ecol 60:363-9. 2007
..campbellii strain. Our data indicate that PHB-accumulating bacteria, such as B. denitrificans PHB2, could be used as an an effective and economically interesting alternative strategy to control infections in aquaculture...
- AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1
Wim De Windt
Laboratory of Microbial Ecology and Technology LabMET, Ghent University, Coupure Links 653, B 9000 Gent, Belgium
Microbiology 152:721-9. 2006
..By complementing this mutation with the vector pCM62, expressing the aggA gene, this effect could be nullified and biofilm formation was restored to at least the level of the MR-1 wild-type...
- Caspase-14 protects against epidermal UVB photodamage and water loss
Geertrui Denecker
Department for Molecular Biomedical Research, VIB, Technologie Park 927, B 9052, Ghent, Belgium
Nat Cell Biol 9:666-74. 2007
..Removal of the stratum corneum indicate that caspase-14 controls the UVB scavenging capacity of the stratum corneum...
