Skip to main content

2017 | OriginalPaper | Buchkapitel

A New Schema to Identify S-farnesyl Cysteine Prenylation Sites with Substrate Motifs

verfasst von : Van-Nui Nguyen, Thi-Xuan Tran, Hai-Minh Nguyen, Hong-Tan Nguyen, Tzong-Yi Lee

Erschienen in: Advances in Information and Communication Technology

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Protein prenylation is the addition of hydrophobic molecules to a protein or chemical compound. It is a post-translational modification that plays very important roles for many cellular processes such as DNA replication, signaling, trafficking, and other cellular functions in eukaryotes. Protein S-farnesyl cysteine prenylation is a specific kind of prenylation involved in the transfer of a farnesyl moiety to a cytoplasmic cysteine at or near the C-terminus of the target protein. Recent advancements in proteomic technology have stimulated an increasing interested in the identification of protein S-farnesyl cysteine prenylation sites. However, there is still a lack of methods proposed for the prediction of S-farnesyl cysteine sites. With a rapidly increasing number of experimentally verified S-farnesyl cysteine sites, it is motivated in proposed new method for identifying S-farnesyl cysteine prenylation sites.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Kamiya, Y., et al.: Structure of rhodotorucine A, a novel lipopeptide, inducing mating tube formation in Rhodosporidium toruloides. Biochem. Biophys. Res. Commun. 83(3), 1077–1083 (1978)CrossRef Kamiya, Y., et al.: Structure of rhodotorucine A, a novel lipopeptide, inducing mating tube formation in Rhodosporidium toruloides. Biochem. Biophys. Res. Commun. 83(3), 1077–1083 (1978)CrossRef
2.
Zurück zum Zitat Farnsworth, C.C., et al.: Human lamin B contains a farnesylated cysteine residue. J. Biol. Chem. 264(34), 20422–20429 (1989) Farnsworth, C.C., et al.: Human lamin B contains a farnesylated cysteine residue. J. Biol. Chem. 264(34), 20422–20429 (1989)
3.
Zurück zum Zitat Wolda, S.L., Glomset, J.A.: Evidence for modification of lamin B by a product of mevalonic acid. J. Biol. Chem. 263(13), 5997–6000 (1988) Wolda, S.L., Glomset, J.A.: Evidence for modification of lamin B by a product of mevalonic acid. J. Biol. Chem. 263(13), 5997–6000 (1988)
4.
Zurück zum Zitat Soni, R., et al.: Structure-based binding between protein farnesyl transferase and PRL-PTP of malaria parasite: an interaction study of prenylation process in Plasmodium. J. Biomol. Struct. Dyn., 1–12 (2016) Soni, R., et al.: Structure-based binding between protein farnesyl transferase and PRL-PTP of malaria parasite: an interaction study of prenylation process in Plasmodium. J. Biomol. Struct. Dyn., 1–12 (2016)
5.
Zurück zum Zitat Novelli, G., D’Apice, M.R.: Protein farnesylation and disease. J. Inherit. Metab. Dis. 35(5), 917–926 (2012)CrossRef Novelli, G., D’Apice, M.R.: Protein farnesylation and disease. J. Inherit. Metab. Dis. 35(5), 917–926 (2012)CrossRef
6.
Zurück zum Zitat Maurer-Stroh, S., et al.: Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput. Biol. 3(4), e66 (2007)CrossRef Maurer-Stroh, S., et al.: Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput. Biol. 3(4), e66 (2007)CrossRef
7.
Zurück zum Zitat Palsuledesai, C.C., Distefano, M.D.: Protein prenylation: enzymes, therapeutics, and biotechnology applications. ACS Chem. Biol. 10(1), 51–62 (2015)CrossRef Palsuledesai, C.C., Distefano, M.D.: Protein prenylation: enzymes, therapeutics, and biotechnology applications. ACS Chem. Biol. 10(1), 51–62 (2015)CrossRef
8.
Zurück zum Zitat Hechinger, A.K., et al.: Inhibition of protein geranylgeranylation and farnesylation protects against graft-versus-host disease via effects on CD4 effector T cells. Haematologica 98(1), 31–40 (2013)CrossRef Hechinger, A.K., et al.: Inhibition of protein geranylgeranylation and farnesylation protects against graft-versus-host disease via effects on CD4 effector T cells. Haematologica 98(1), 31–40 (2013)CrossRef
9.
Zurück zum Zitat Charron, G., et al.: Prenylome profiling reveals S-farnesylation is crucial for membrane targeting and antiviral activity of ZAP long-isoform. Proc. Natl. Acad. Sci. USA 110(27), 11085–11090 (2013)CrossRef Charron, G., et al.: Prenylome profiling reveals S-farnesylation is crucial for membrane targeting and antiviral activity of ZAP long-isoform. Proc. Natl. Acad. Sci. USA 110(27), 11085–11090 (2013)CrossRef
10.
Zurück zum Zitat Geryk-Hall, M., Yang, Y., Hughes, D.P.: Driven to death: inhibition of farnesylation increases Ras activity and promotes growth arrest and cell death [corrected]. Mol. Cancer Ther. 9(5), 1111–1119 (2010)CrossRef Geryk-Hall, M., Yang, Y., Hughes, D.P.: Driven to death: inhibition of farnesylation increases Ras activity and promotes growth arrest and cell death [corrected]. Mol. Cancer Ther. 9(5), 1111–1119 (2010)CrossRef
11.
Zurück zum Zitat Goodsell, D.S.: The molecular perspective: protein farnesyltransferase. Oncologist 8(6), 597–598 (2003)CrossRef Goodsell, D.S.: The molecular perspective: protein farnesyltransferase. Oncologist 8(6), 597–598 (2003)CrossRef
12.
Zurück zum Zitat Einav, S., Glenn, J.S.: Prenylation inhibitors: a novel class of antiviral agents. J. Antimicrob. Chemother. 52(6), 883–886 (2003)CrossRef Einav, S., Glenn, J.S.: Prenylation inhibitors: a novel class of antiviral agents. J. Antimicrob. Chemother. 52(6), 883–886 (2003)CrossRef
13.
Zurück zum Zitat Xie, Y., et al.: GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites, Scientific reports, 6, 28249 (2016) Xie, Y., et al.: GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites, Scientific reports, 6, 28249 (2016)
14.
Zurück zum Zitat Maurer-Stroh, S., Eisenhaber, F.: Refinement and prediction of protein prenylation motifs. Genome Biol. 6(6), R55 (2005)CrossRef Maurer-Stroh, S., Eisenhaber, F.: Refinement and prediction of protein prenylation motifs. Genome Biol. 6(6), R55 (2005)CrossRef
15.
Zurück zum Zitat Chen, W.N., et al.: Particle swarm optimization with an aging leader and challengers. IEEE Trans. Evol. Comput. 17(2), 241–258 (2013)CrossRef Chen, W.N., et al.: Particle swarm optimization with an aging leader and challengers. IEEE Trans. Evol. Comput. 17(2), 241–258 (2013)CrossRef
16.
Zurück zum Zitat Nguyen, V.N., et al.: A new scheme to characterize and identify protein ubiquitination sites. In: IEEE/ACM transactions on computational biology and bioinformatics IEEE, ACM (2016) Nguyen, V.N., et al.: A new scheme to characterize and identify protein ubiquitination sites. In: IEEE/ACM transactions on computational biology and bioinformatics IEEE, ACM (2016)
17.
Zurück zum Zitat Nguyen, V.N., et al.: Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. BMC Bioinform. 16(Suppl. 1), S1 (2015)CrossRef Nguyen, V.N., et al.: Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. BMC Bioinform. 16(Suppl. 1), S1 (2015)CrossRef
18.
Zurück zum Zitat Lee, T.Y., et al.: Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. Bioinformatics 27(13), 1780–1787 (2011)CrossRef Lee, T.Y., et al.: Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. Bioinformatics 27(13), 1780–1787 (2011)CrossRef
19.
Zurück zum Zitat Lee, T.Y., et al.: SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS One 6(7), e21849 (2011)CrossRef Lee, T.Y., et al.: SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity. PLoS One 6(7), e21849 (2011)CrossRef
20.
Zurück zum Zitat Boeckmann, B., et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31(1), 365–370 (2003)CrossRef Boeckmann, B., et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31(1), 365–370 (2003)CrossRef
21.
Zurück zum Zitat Lu, C.T., et al.: DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res. 41(Database issue), D295–D305 (2013) Lu, C.T., et al.: DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res. 41(Database issue), D295–D305 (2013)
22.
Zurück zum Zitat Keshava Prasad, T.S., et al.: Human protein reference database–2009 update. Nucleic Acids Res. 37(Database issue), D767–D772 (2009) Keshava Prasad, T.S., et al.: Human protein reference database–2009 update. Nucleic Acids Res. 37(Database issue), D767–D772 (2009)
23.
Zurück zum Zitat Huang, Y., et al.: CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 26(5), 680–682 (2010)CrossRef Huang, Y., et al.: CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 26(5), 680–682 (2010)CrossRef
24.
Zurück zum Zitat Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)CrossRef Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)CrossRef
25.
Zurück zum Zitat Chang, C.-C., Lin, C.-J.: LIBSVM: a library for support vector machines. ACM Trans. Intell. Syst. Technol. 2 (2011) Chang, C.-C., Lin, C.-J.: LIBSVM: a library for support vector machines. ACM Trans. Intell. Syst. Technol. 2 (2011)
26.
Zurück zum Zitat Nguyen, V.N., et al.: UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. Database : J. Biol. Databases and Curation (2016) Nguyen, V.N., et al.: UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. Database : J. Biol. Databases and Curation (2016)
27.
Zurück zum Zitat Matthews, B.W.: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405(2), 442–451 (1975)CrossRef Matthews, B.W.: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405(2), 442–451 (1975)CrossRef
28.
Zurück zum Zitat Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268(1), 78–94 (1997)CrossRef Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268(1), 78–94 (1997)CrossRef
29.
Zurück zum Zitat Crooks, G.E., et al.: WebLogo: a sequence logo generator. Genome Res. 14(6), 1188–1190 (2004)CrossRef Crooks, G.E., et al.: WebLogo: a sequence logo generator. Genome Res. 14(6), 1188–1190 (2004)CrossRef
30.
Zurück zum Zitat Vacic, V., Iakoucheva, L.M., Radivojac, P.: Two sample logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22(12), 1536–1537 (2006)CrossRef Vacic, V., Iakoucheva, L.M., Radivojac, P.: Two sample logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22(12), 1536–1537 (2006)CrossRef
31.
Zurück zum Zitat Tung, C.W., Ho, S.Y.: Computational identification of ubiquitylation sites from protein sequences. BMC Bioinform. 9, 310 (2008)CrossRef Tung, C.W., Ho, S.Y.: Computational identification of ubiquitylation sites from protein sequences. BMC Bioinform. 9, 310 (2008)CrossRef
Metadaten
Titel
A New Schema to Identify S-farnesyl Cysteine Prenylation Sites with Substrate Motifs
verfasst von
Van-Nui Nguyen
Thi-Xuan Tran
Hai-Minh Nguyen
Hong-Tan Nguyen
Tzong-Yi Lee
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-49073-1_10