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Novel technologies for the analysis of protein complexes

Kevin Titeca (UGent)
(2017)
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Abstract
All functions in the cell result from the complex and dynamic collaboration of biomolecules, with a central role for the interactions between proteins. Protein–protein interactions (PPIs) connect genotypes with phenotypes, and disruption often causes disease. The study of PPIs allows to answer fundamental biological questions and to generate new hypotheses on the functions of proteins. Several technologies already exist to detect PPIs, but there is still room for improvement. We here describe Virotrap and the straightforward filtering index (SFINX). Virotrap is a novel complementary PPI technology that avoids the need for cell lysis by trapping the protein complexes in virus-like particles (VLPs). The technology exploits the ability of the Gag protein of the human immunodeficiency virus (HIV) to induce budding of vesicles without any need for other viral proteins. By genetically fusing the protein of interest to the Gag protein, Virotrap successfully captures its interaction partners in the VLPs, whereafter the VLPs can be purified and the interactors can be identified. Similar to most PPI technologies, Virotrap however also yields false interactors. The novel software approach SFINX aims to separate the true interactors from the false ones in a highly accurate, fast and user-friendly way for datasets resulting from mass spectrometry based PPI technologies, such as Virotrap and affinity purification – mass spectrometry. SFINX outperforms alternative filter technologies on two benchmark datasets, and it is easily accessible via its website interface at http://sfinx.ugent.be/ or as an R package from the comprehensive R archive network (CRAN). We hope that Virotrap and SFINX will enhance the research of many, laying the foundation for further scientific discovery and technological innovation.
Keywords
protein-protein interactions, interactomics, proteomics, false positives, interactomics filtering

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Citation

Please use this url to cite or link to this publication:

Chicago
Titeca, Kevin. 2017. “Novel Technologies for the Analysis of Protein Complexes”. Ghent, Belgium: Ghent University. Faculty of Medicine and Health Sciences.
APA
Titeca, Kevin. (2017). Novel technologies for the analysis of protein complexes. Ghent University. Faculty of Medicine and Health Sciences, Ghent, Belgium.
Vancouver
1.
Titeca K. Novel technologies for the analysis of protein complexes. [Ghent, Belgium]: Ghent University. Faculty of Medicine and Health Sciences; 2017.
MLA
Titeca, Kevin. “Novel Technologies for the Analysis of Protein Complexes.” 2017 : n. pag. Print.
@phdthesis{8514867,
  abstract     = {All functions in the cell result from the complex and dynamic collaboration of biomolecules, with a central role for the interactions between proteins. Protein--protein interactions (PPIs) connect genotypes with phenotypes, and disruption often causes disease. The study of PPIs allows to answer fundamental biological questions and to generate new hypotheses on the functions of proteins. Several technologies already exist to detect PPIs, but there is still room for improvement. We here describe Virotrap and the straightforward filtering index (SFINX). Virotrap is a novel complementary PPI technology that avoids the need for cell lysis by trapping the protein complexes in virus-like particles (VLPs). The technology exploits the ability of the Gag protein of the human immunodeficiency virus (HIV) to induce budding of vesicles without any need for other viral proteins. By genetically fusing the protein of interest to the Gag protein, Virotrap successfully captures its interaction partners in the VLPs, whereafter the VLPs can be purified and the interactors can be identified. Similar to most PPI technologies, Virotrap however also yields false interactors. The novel software approach SFINX aims to separate the true interactors from the false ones in a highly accurate, fast and user-friendly way for datasets resulting from mass spectrometry based PPI technologies, such as Virotrap and affinity purification -- mass spectrometry. SFINX outperforms alternative filter technologies on two benchmark datasets, and it is easily accessible via its website interface at http://sfinx.ugent.be/ or as an R package from the comprehensive R archive network (CRAN). We hope that Virotrap and SFINX will enhance the research of many, laying the foundation for further scientific discovery and technological innovation.
},
  author       = {Titeca, Kevin},
  language     = {eng},
  pages        = {201},
  publisher    = {Ghent University. Faculty of Medicine and Health Sciences},
  school       = {Ghent University},
  title        = {Novel technologies for the analysis of protein complexes},
  year         = {2017},
}