Petra Van Damme

Summary

Publications

  1. ncbi request reprint A Saccharomyces cerevisiae Model Reveals In Vivo Functional Impairment of the Ogden Syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant
    Petra Van Damme
    From the Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium Department of Biochemistry, Ghent University, B 9000 Ghent, Belgium
    Mol Cell Proteomics 13:2031-41. 2014
  2. pmc N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB
    Petra 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
  3. doi request reprint 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
  4. doi request reprint Protein alpha-N-acetylation studied by N-terminomics
    Petra Van Damme
    Department of Medical Protein Research, VIB, Ghent, Belgium
    FEBS J 278:3822-34. 2011
  5. pmc 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
  6. doi request reprint 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
  7. ncbi request reprint MS-driven protease substrate degradomics
    Francis Impens
    Department of Medical Protein Research, VIB, Ghent, Belgium
    Proteomics 10:1284-96. 2010
  8. pmc Conservation of the extended substrate specificity profiles among homologous granzymes across species
    Kim Plasman
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 12:2921-34. 2013
  9. pmc 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
  10. pmc 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

Collaborators

Detail Information

Publications41

  1. ncbi request reprint A Saccharomyces cerevisiae Model Reveals In Vivo Functional Impairment of the Ogden Syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant
    Petra Van Damme
    From the Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium Department of Biochemistry, Ghent University, B 9000 Ghent, Belgium
    Mol Cell Proteomics 13:2031-41. 2014
    ..For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA. ..
  2. pmc N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB
    Petra 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
    ....
  3. doi request reprint 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...
  4. doi request reprint Protein alpha-N-acetylation studied by N-terminomics
    Petra 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...
  5. pmc 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...
  6. doi request reprint 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...
  7. ncbi request reprint 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...
  8. pmc Conservation of the extended substrate specificity profiles among homologous granzymes across species
    Kim Plasman
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 12:2921-34. 2013
    ..Our results thus indicate a conserved, but hitherto underappreciated specificity-determining role of extended protease-substrate contacts in steering cleavage susceptibility. ..
  9. pmc 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...
  10. pmc 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...
  11. ncbi request reprint A la carte proteomics with an emphasis on gel-free techniques
    Kris 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...
  12. pmc 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...
  13. ncbi request reprint 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...
  14. pmc The Arabidopsis metacaspase9 degradome
    Liana Tsiatsiani
    Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
    Plant Cell 25:2831-47. 2013
    ....
  15. ncbi request reprint 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...
  16. ncbi request reprint 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...
  17. doi request reprint 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
    ....
  18. doi request reprint 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
    ....
  19. doi request reprint 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...
  20. ncbi request reprint 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...
  21. doi request reprint 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...
  22. doi request reprint 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...
  23. doi request reprint 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...
  24. doi request reprint 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...
  25. ncbi request reprint 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...
  26. doi request reprint 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...
  27. pmc Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events
    Gerben Menschaert
    Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
    Mol Cell Proteomics 12:1780-90. 2013
    ..The underlying mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000124. ..
  28. doi request reprint 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
    ....
  29. ncbi request reprint 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...
  30. pmc 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
    ....
  31. ncbi request reprint 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
    ....
  32. doi request reprint 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...
  33. pmc 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...
  34. doi request reprint 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...
  35. ncbi request reprint Holistic view on the extended substrate specificities of orthologous granzymes
    Kim Plasman
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    J Proteome Res 13:1785-93. 2014
    ....
  36. pmc 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
    ....
  37. pmc N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men
    Petra Van Damme
    Department of Medical Protein Research, VIB, B 9000 Ghent, Belgium
    Mol Cell Proteomics 13:1245-61. 2014
    ..Finally, TargetP analysis predicted that the usage of aTIS often results in altered subcellular localization patterns, providing a mechanism for functional diversification. ..
  38. ncbi request reprint 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...
  39. ncbi request reprint 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...
  40. ncbi request reprint 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...