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PepShell : visualization of conformational proteomics data

(2015) JOURNAL OF PROTEOME RESEARCH. 14(4). p.1987-1990
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based approaches, such as limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labeling, are frequently used to characterize protein conformation and dynamics, yet the interpretation of these data can be cumbersome and time consuming. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based conformational proteomics studies by visualization of the identified peptides both at the sequence and structure levels. Moreover, PepShell allows the comparison of experiments under different conditions, including different proteolysis times or binding of the protein to different substrates or inhibitors.
Keywords
ENSEMBLES, NMR, DYNAMICS, MTMDAT, PROTEIN, ASSEMBLIES, LIMITED PROTEOLYSIS, HYDROGEN-DEUTERIUM EXCHANGE, MASS-SPECTROMETRY DATA, protein structure, PepShell, visualization of peptides, conformational proteomics, Comparison of peptides

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Chicago
Vandermarliere, Elien, Davy Maddelein, Niels Hulstaert, Elisabeth Stes, Michela Di Michele, Kris Gevaert, Edgar Jacoby, Dirk Brehmer, and Lennart Martens. 2015. “PepShell : Visualization of Conformational Proteomics Data.” Journal of Proteome Research 14 (4): 1987–1990.
APA
Vandermarliere, E., Maddelein, D., Hulstaert, N., Stes, E., Di Michele, M., Gevaert, K., Jacoby, E., et al. (2015). PepShell : visualization of conformational proteomics data. JOURNAL OF PROTEOME RESEARCH, 14(4), 1987–1990.
Vancouver
1.
Vandermarliere E, Maddelein D, Hulstaert N, Stes E, Di Michele M, Gevaert K, et al. PepShell : visualization of conformational proteomics data. JOURNAL OF PROTEOME RESEARCH. 2015;14(4):1987–90.
MLA
Vandermarliere, Elien, Davy Maddelein, Niels Hulstaert, et al. “PepShell : Visualization of Conformational Proteomics Data.” JOURNAL OF PROTEOME RESEARCH 14.4 (2015): 1987–1990. Print.
@article{5987437,
  abstract     = {Proteins are dynamic molecules; they undergo crucial conformational changes induced by post-translational modifications and by binding of cofactors or other molecules. The characterization of these conformational changes and their relation to protein function is a central goal of structural biology. Unfortunately, most conventional methods to obtain structural information do not provide information on protein dynamics. Therefore, mass spectrometry-based approaches, such as limited proteolysis, hydrogen-deuterium exchange, and stable-isotope labeling, are frequently used to characterize protein conformation and dynamics, yet the interpretation of these data can be cumbersome and time consuming. Here, we present PepShell, a tool that allows interactive data analysis of mass spectrometry-based conformational proteomics studies by visualization of the identified peptides both at the sequence and structure levels. Moreover, PepShell allows the comparison of experiments under different conditions, including different proteolysis times or binding of the protein to different substrates or inhibitors.},
  author       = {Vandermarliere, Elien and Maddelein, Davy and Hulstaert, Niels and Stes, Elisabeth and Di Michele, Michela and Gevaert, Kris and Jacoby, Edgar and Brehmer, Dirk and Martens, Lennart},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {ENSEMBLES,NMR,DYNAMICS,MTMDAT,PROTEIN,ASSEMBLIES,LIMITED PROTEOLYSIS,HYDROGEN-DEUTERIUM EXCHANGE,MASS-SPECTROMETRY DATA,protein structure,PepShell,visualization of peptides,conformational proteomics,Comparison of peptides},
  language     = {eng},
  number       = {4},
  pages        = {1987--1990},
  title        = {PepShell : visualization of conformational proteomics data},
  url          = {http://dx.doi.org/10.1021/pr5012125},
  volume       = {14},
  year         = {2015},
}

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