TopFIND 2.0—linking protein termini with proteolytic processing and modifications altering protein function
作者： P. F. Lange , P. F. Huesgen , C. M. Overall
DOI: 10.1093/NAR/GKR1025
关键词: Protein domain 、 Proteolytic enzymes 、 UniProt 、 Proteome 、 Biochemistry 、 Saccharomyces cerevisiae 、 Protein tertiary structure 、 Biology 、 Proteomics 、 MEROPS
摘要: Protein termini provide critical insights into the functional state of individual proteins. With recent advances in specific proteomics approaches to enrich for N- and C-terminomes, global analysis whole terminomes at a proteome-wide scale is now possible. Information on actual C-termini proteins vivo any post-translational modifications, including their generation by proteolytic processing, rapidly accumulating. To access this information we present version 2.0 TopFIND (http://clipserve.clip.ubc.ca/topfind), knowledgebase protein termini, terminus modifications underlying processing. Built protein-centric framework covers five species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae Escherichia coli incorporates from curated community submissions, publications, UniProtKB MEROPS. Emphasis placed detailed description classification evidence supporting reported identification each cleavage site, modification. A suite filters can be applied select evidence. dynamic network representation relationship between proteases, substrates inhibitors as well visualization protease site specificities complements displayed. Hence, supports depth investigation spark new hypotheses function correlating events with domains mutations.
oup.com
paperity.org
oxfordjournals.org参考文章(40)
Victor Quesada, Gonzalo R Ordonez, Luis M Sanchez, Xose S Puente, Carlos López-Otín, The Degradome database: mammalian proteases and diseases of proteolysis. Nucleic Acids Research. ,vol. 37, pp. 239- 243 ,(2009) , 10.1093/NAR/GKN570
Christopher M. Overall, Oded Kleifeld, Validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy Nature Reviews Cancer. ,vol. 6, pp. 227- 239 ,(2006) , 10.1038/NRC1821
Jennifer H. Cox, Richard A. Dean, Clive R. Roberts, Christopher M. Overall, Matrix metalloproteinase processing of CXCL11/I-TAC results in loss of chemoattractant activity and altered glycosaminoglycan binding. Journal of Biological Chemistry. ,vol. 283, pp. 19389- 19399 ,(2008) , 10.1074/JBC.M800266200
Georgina S. Butler, Christopher M. Overall, Proteomic identification of multitasking proteins in unexpected locations complicates drug targeting Nature Reviews Drug Discovery. ,vol. 8, pp. 935- 948 ,(2009) , 10.1038/NRD2945
Luisa Montecchi-Palazzi, Ron Beavis, Pierre-Alain Binz, Robert J Chalkley, John Cottrell, David Creasy, Jim Shofstahl, Sean L Seymour, John S Garavelli, The PSI-MOD community standard for representation of protein modification data Nature Biotechnology. ,vol. 26, pp. 864- 866 ,(2008) , 10.1038/NBT0808-864
Petra Van Damme, Lennart Martens, Jozef Van Damme, Koen Hugelier, An Staes, Joël Vandekerckhove, Kris Gevaert, Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nature Methods. ,vol. 2, pp. 771- 777 ,(2005) , 10.1038/NMETH792
G. Xu, S. B. Y. Shin, S. R. Jaffrey, Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini Proceedings of the National Academy of Sciences of the United States of America. ,vol. 106, pp. 19310- 19315 ,(2009) , 10.1073/PNAS.0908958106
Lucy McDonald, Duncan H L Robertson, Jane L Hurst, Robert J Beynon, Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides Nature Methods. ,vol. 2, pp. 955- 957 ,(2005) , 10.1038/NMETH811
Kris Gevaert, Marc Goethals, Lennart Martens, Jozef Van Damme, An Staes, Grégoire R. Thomas, Joël Vandekerckhove, Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nature Biotechnology. ,vol. 21, pp. 566- 569 ,(2003) , 10.1038/NBT810
Thierry Meinnel, Carmela Giglione, Tools for analyzing and predicting N‐terminal protein modifications Proteomics. ,vol. 8, pp. 626- 649 ,(2008) , 10.1002/PMIC.200700592