Protein localization prediction

The protein subcellular localization prediction includes biochemical and bioinformatics methods for the determination of the target compartment of a protein .

properties

In eukaryotes, proteins are often sorted on the basis of their signal sequences after their production in the cytosol and supplied to their destination. The target location can be a cellular compartment such as the cell nucleus , the endoplasmic reticulum , the mitochondria , possibly the chloroplasts , the peroxisomes , or it can be outside the cell (in the case of exocytosis and secretion ).

In prokaryotes , proteins are transported or secreted into the periplasm , among other things .

The localization of a protein can be determined experimentally by fluorescence microscopy or by protein sequencing (based on the signal sequences); it can also be predicted in silico bioinformatically.

Methods

The characteristic predictors depend on the respective species . Below are some methods for predicting protein localization:

Cell-PLoc
BaCelLo
CELLO
ClubSub-P
Euk-mPLoc 2.0
CoBaltDB
HSLpred
KnowPredsite
LOCtree
LocTree2 / 3
MultiLoc
PSORT
PSORTb
MetaLocGramN
PredictNLS
Proteome Analyst
SCLPred
SecretomeP
SherLoc
TargetP
TMHMM
WoLF PSORT
APSLAP

Applications

Prediction of the localization of proteins is used in biochemistry and biotechnology in the generation of secreted recombinant proteins . In pharmacology , secreted proteins and membrane proteins are often targets in a drug design . Proteins with incorrect localization can be found in cancer and Alzheimer's disease , among others .

literature

Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y: Predicting function: from genes to genomes and back . In: J. Mol. Biol. . 283, No. 4, November 1998, pp. 707-25. doi : 10.1006 / jmbi.1998.2144 . PMID 9790834 .
Nakai K: Protein sorting signals and prediction of subcellular localization . In: Adv Protein Chem.. . 54, 2000, pp. 277-344. doi : 10.1016 / s0065-3233 (00) 54009-1 . PMID 10829231 .
Emanuelsson O: Predicting protein subcellular localization from amino acid sequence information . In: letter. Bioinformatics . 3, No. 4, December 2002, pp. 361-76. doi : 10.1093 / bib / 3.4.361 . PMID 12511065 .
Schneider G, Fechner U: Advances in the prediction of protein targeting signals . In: Proteomics . 4, No. 6, June 2004, pp. 1571-1580. doi : 10.1002 / pmic.200300786 . PMID 15174127 .
Gardy JL, Brinkman FS: Methods for predicting bacterial protein subcellular localization . In: Nat. Rev. Microbiol. . 4, No. 10, October 2006, pp. 741-51. doi : 10.1038 / nrmicro1494 . PMID 16964270 .
Chou KC, Shen HB: Recent progress in protein subcellular location prediction . In: Anal. Biochem. . 370, No. 1, November 2007, pp. 1-16. doi : 10.1016 / year from 2007.07.006 . PMID 17698024 .

Web links

Cell Centered Database - Protein subcellular localization data
Cell-PLoc 2.0 - A recently updated version of Cell-PLoc
BaCelLo - Balanced subCellular Localization predictor
CELLO - subCELlular LOcalization predictor for prokaryotes and eukaryotes
LocTree2 / 3 - prediction web server for proteins in all domains of life
MultiLoc - MultiLoc prediction web server
PSORT.org - A portal for protein subcellular localization predictors
SherLoc - SherLoc prediction webserver

Individual evidence

↑ Rey S, Gardy JL, Brinkman FS: Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria . In: BMC Genomics . 6, 2005, p. 162. doi : 10.1186 / 1471-2164-6-162 . PMID 16288665 . PMC 1314894 (free full text).
↑ ^a ^b Chou KC, Shen HB: Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms (updated version: Cell-PLoc 2.0: An improved package of web servers for predicting subcellular localization of proteins in various organisms, Natural Science, 2010, 2, 1090-1103) . In: Nat Protoc . 3, No. 2, 2008, pp. 153-62. doi : 10.1038 / nprot.2007.494 . PMID 18274516 .
↑ Chou, KC; Wu, ZC; Xiao, X. iLoc-Euk: A Multi-Label Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Eukaryotic Proteins, PLoS ONE, 2011, 6, e18258.
↑ Shen HB, Chou KC: A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0 . In: Anal. Biochem. . 394, No. 2, November 2009, pp. 269-74. doi : 10.1016 / year from 2009.07.046 . PMID 19651102 .
↑ Chou KC, Shen HB: Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization . In: PLoS ONE . 5, No. 6, 2010, p. E11335. doi : 10.1371 / journal.pone.0011335 . PMID 20596258 . PMC 2893129 (free full text).
↑ Gardy JL, Brinkman FS: Methods for predicting bacterial protein subcellular localization . In: Nat. Rev. Microbiol. . 4, No. 10, October 2006, pp. 741-51. doi : 10.1038 / nrmicro1494 . PMID 16964270 .
↑ Nakai, K. Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem., 2000, 54, 277-344.
↑ Chou, KC; Shen, HB Review: "Recent progresses in protein subcellular location prediction" Anal. Biochem 2007, 370, 1-16.
↑ Pierleoni A, Martelli PL, Fariselli P, Casadio R: BaCelLo: a balanced subcellular localization predictor . In: Bioinformatics . 22, No. 14, July 2006, pp. E408–16. doi : 10.1093 / bioinformatics / btl222 . PMID 16873501 .
↑ Yu CS, Lin CJ, Hwang JK: Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions . In: Protein Sci. . 13, No. 5, May 2004, pp. 1402-6. doi : 10.1110 / ps.03479604 . PMID 15096640 . PMC 2286765 (free full text).
↑ Yu CS, Chen YC, Lu CH, Hwang JK: Prediction of protein subcellular localization . In: Proteins . 64, No. 3, August 2006, pp. 643-51. doi : 10.1002 / prot.21018 . PMID 16752418 .
↑ Nagarajan Paramasivam, Dirk Linke: ClubSub-P is a database of cluster-based subcellular localization (SCL) predictions for Archaea and Gram negative bacteria . In: Frontiers in Microbiology . 2, 2011. doi : 10.3389 / fmicb.2011.00218 . PMID 22073040 .
↑ Chou KC, Shen HB: A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0 . In: PLoS ONE . 5, No. 4, 2010, p. E9931. doi : 10.1371 / journal.pone.0009931 . PMID 20368981 . PMC 2848569 (free full text).
↑ Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F: CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources . In: BMC Microbiol. . 10, 2010, p. 88. doi : 10.1186 / 1471-2180-10-88 . PMID 20331850 . PMC 2850352 (free full text).
↑ Garg A, Bhasin M, Raghava GP: Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search . In: J. Biol. Chem. . 280, No. 15, April 2005, pp. 14427-32. doi : 10.1074 / jbc.M411789200 . PMID 15647269 .
↑ Lin HN, Chen CT, Sung TY, Ho SY, and Hsu WL .: Protein subcellular localization prediction of eukaryotes using a knowledge-based approach . In: BMC Bioinformatics. . 10, December 2009, p. S8. doi : 10.1186 / 1471-2105-10-S15-S8 . PMID 19958518 .
^ Nair R, Rost B: Mimicking cellular sorting improves prediction of subcellular localization . In: J. Mol. Biol. . 348, No. 1, April 2005, pp. 85-100. doi : 10.1016 / j.jmb.2005.02.025 . PMID 15808855 .
^ Goldberg T, Hamp T, Rost B: LocTree2 predicts localization for all domains of life . In: Bioinformatics . 28, 2012, pp. I458-i465. doi : 10.1093 / bioinformatics / bts390 . PMID 22962467 .
↑ Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Nielsen H, Rost B et al. : LocTree3 prediction of localization . In: Nucleic Acids Research . 2014. doi : 10.1093 / nar / gku396 . PMID 24848019 .
↑ Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O: MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition . In: Bioinformatics . 22, No. 10, May 2006, pp. 1158-1165. doi : 10.1093 / bioinformatics / btl002 . PMID 16428265 .
↑ Nakai K, Kanehisa M: Expert system for predicting protein localization sites in gram-negative bacteria . In: Proteins . 11, No. 2, 1991, pp. 95-110. doi : 10.1002 / prot.340110203 . PMID 1946347 .
↑ Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS: PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria . In: Nucleic Acids Res . 31, No. 13, July 2003, pp. 3613-7. doi : 10.1093 / nar / gkg602 . PMID 12824378 . PMC 169008 (free full text).
↑ Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS: PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis . In: Bioinformatics . 21, No. 5, March 2005, pp. 617-23. doi : 10.1093 / bioinformatics / bti057 . PMID 15501914 .
↑ Magnus M, Pawlowski M, Bujnicki JM: MetaLocGramN: a meta-predictor of protein subcellular localization for Gram-negative bacteria . In: BBA - Proteins and Proteomics . 1824, No. 12, December 2012, pp. 1425-1433. doi : 10.1016 / j.bbapap.2012.05.018 . PMID 22705560 .
^ Nair R, Carter P, Rost B: NLSdb: database of nuclear localization signals . In: Nucleic Acids Res . 31, No. 1, January 2003, pp. 397-9. doi : 10.1093 / nar / gkg001 . PMID 12520032 . PMC 165448 (free full text).
↑ Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R: Predicting Subcellular localization of proteins using machine-learned classifier . In: Bioinformatics . 20, No. 4, March 2004, pp. 547-56. PMID 14990451 .
^ Mooney C, Wang YH, Pollastri G .: SCLpred: protein subcellular localization prediction by N-to-1 neural networks. . In: Bioinformatics . 27, No. 20, October 2011, pp. 2812-9. doi : 10.1093 / bioinformatics / btr494 . PMID 21873639 .
↑ Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S: Feature-based prediction of non-classical and leaderless protein secretion . In: Protein Eng. Of. Sel. . 17, No. 4, April 2004, pp. 349-56. doi : 10.1093 / protein / gzh037 . PMID 15115854 .
↑ Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O: SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data . In: Bioinformatics . 23, No. 11, June 2007, pp. 1410-7. doi : 10.1093 / bioinformatics / btm115 . PMID 17392328 .
↑ Emanuelsson O, Nielsen H, Brunak S, von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence . In: J. Mol. Biol. . 300, No. 4, July 2000, pp. 1005-1016. doi : 10.1006 / jmbi.2000.3903 . PMID 10891285 .
↑ Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K: WoLF PSORT: protein localization predictor . In: Nucleic Acids Res . 35, No. Web Server issue, July 2007, pp. W585-7. doi : 10.1093 / nar / gkm259 . PMID 17517783 . PMC 1933216 (free full text).
↑ Saravanan V, Lakshmi PTV: APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein . In: Acta Biotheor . 61, No. 4, Dec 2013, pp. 481-497. doi : 10.1007 / s10441-013-9197-1 . PMID 23982307 .

[pmid16288665-1] Rey S, Gardy JL, Brinkman FS: Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria . In: BMC Genomics . 6, 2005, p. 162. doi : 10.1186 / 1471-2164-6-162 . PMID 16288665 . PMC 1314894 (free full text).

[chou1-2] Chou KC, Shen HB: Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms (updated version: Cell-PLoc 2.0: An improved package of web servers for predicting subcellular localization of proteins in various organisms, Natural Science, 2010, 2, 1090-1103) . In: Nat Protoc . 3, No. 2, 2008, pp. 153-62. doi : 10.1038 / nprot.2007.494 . PMID 18274516 .

[3] Chou, KC; Wu, ZC; Xiao, X. iLoc-Euk: A Multi-Label Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Eukaryotic Proteins, PLoS ONE, 2011, 6, e18258.

[pmid19651102-4] Shen HB, Chou KC: A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0 . In: Anal. Biochem. . 394, No. 2, November 2009, pp. 269-74. doi : 10.1016 / year from 2009.07.046 . PMID 19651102 .

[pmid20596258-5] Chou KC, Shen HB: Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization . In: PLoS ONE . 5, No. 6, 2010, p. E11335. doi : 10.1371 / journal.pone.0011335 . PMID 20596258 . PMC 2893129 (free full text).

[pmid16964270-6] Gardy JL, Brinkman FS: Methods for predicting bacterial protein subcellular localization . In: Nat. Rev. Microbiol. . 4, No. 10, October 2006, pp. 741-51. doi : 10.1038 / nrmicro1494 . PMID 16964270 .

[7] Nakai, K. Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem., 2000, 54, 277-344.

[8] Chou, KC; Shen, HB Review: "Recent progresses in protein subcellular location prediction" Anal. Biochem 2007, 370, 1-16.

[pmid16873501-9] Pierleoni A, Martelli PL, Fariselli P, Casadio R: BaCelLo: a balanced subcellular localization predictor . In: Bioinformatics . 22, No. 14, July 2006, pp. E408–16. doi : 10.1093 / bioinformatics / btl222 . PMID 16873501 .

[pmid15096640-10] Yu CS, Lin CJ, Hwang JK: Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions . In: Protein Sci. . 13, No. 5, May 2004, pp. 1402-6. doi : 10.1110 / ps.03479604 . PMID 15096640 . PMC 2286765 (free full text).

[pmid16752418-11] Yu CS, Chen YC, Lu CH, Hwang JK: Prediction of protein subcellular localization . In: Proteins . 64, No. 3, August 2006, pp. 643-51. doi : 10.1002 / prot.21018 . PMID 16752418 .

[pmid22073040-12] Nagarajan Paramasivam, Dirk Linke: ClubSub-P is a database of cluster-based subcellular localization (SCL) predictions for Archaea and Gram negative bacteria . In: Frontiers in Microbiology . 2, 2011. doi : 10.3389 / fmicb.2011.00218 . PMID 22073040 .

[chou2-13] Chou KC, Shen HB: A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0 . In: PLoS ONE . 5, No. 4, 2010, p. E9931. doi : 10.1371 / journal.pone.0009931 . PMID 20368981 . PMC 2848569 (free full text).

[pmid20331850-14] Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F: CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources . In: BMC Microbiol. . 10, 2010, p. 88. doi : 10.1186 / 1471-2180-10-88 . PMID 20331850 . PMC 2850352 (free full text).

[pmid15647269-15] Garg A, Bhasin M, Raghava GP: Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search . In: J. Biol. Chem. . 280, No. 15, April 2005, pp. 14427-32. doi : 10.1074 / jbc.M411789200 . PMID 15647269 .

[pmid19958518-16] Lin HN, Chen CT, Sung TY, Ho SY, and Hsu WL .: Protein subcellular localization prediction of eukaryotes using a knowledge-based approach . In: BMC Bioinformatics. . 10, December 2009, p. S8. doi : 10.1186 / 1471-2105-10-S15-S8 . PMID 19958518 .

[pmid15808855-17] Nair R, Rost B: Mimicking cellular sorting improves prediction of subcellular localization . In: J. Mol. Biol. . 348, No. 1, April 2005, pp. 85-100. doi : 10.1016 / j.jmb.2005.02.025 . PMID 15808855 .

[pmid22962467-18] Goldberg T, Hamp T, Rost B: LocTree2 predicts localization for all domains of life . In: Bioinformatics . 28, 2012, pp. I458-i465. doi : 10.1093 / bioinformatics / bts390 . PMID 22962467 .

[pmid24848019-19] Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Nielsen H, Rost B et al. : LocTree3 prediction of localization . In: Nucleic Acids Research . 2014. doi : 10.1093 / nar / gku396 . PMID 24848019 .

[pmid16428265-20] Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O: MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition . In: Bioinformatics . 22, No. 10, May 2006, pp. 1158-1165. doi : 10.1093 / bioinformatics / btl002 . PMID 16428265 .

[pmid1946347-21] Nakai K, Kanehisa M: Expert system for predicting protein localization sites in gram-negative bacteria . In: Proteins . 11, No. 2, 1991, pp. 95-110. doi : 10.1002 / prot.340110203 . PMID 1946347 .

[pmid12824378-22] Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS: PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria . In: Nucleic Acids Res . 31, No. 13, July 2003, pp. 3613-7. doi : 10.1093 / nar / gkg602 . PMID 12824378 . PMC 169008 (free full text).

[pmid15501914-23] Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS: PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis . In: Bioinformatics . 21, No. 5, March 2005, pp. 617-23. doi : 10.1093 / bioinformatics / bti057 . PMID 15501914 .

[pmid22705560-24] Magnus M, Pawlowski M, Bujnicki JM: MetaLocGramN: a meta-predictor of protein subcellular localization for Gram-negative bacteria . In: BBA - Proteins and Proteomics . 1824, No. 12, December 2012, pp. 1425-1433. doi : 10.1016 / j.bbapap.2012.05.018 . PMID 22705560 .

[pmid12520032-25] Nair R, Carter P, Rost B: NLSdb: database of nuclear localization signals . In: Nucleic Acids Res . 31, No. 1, January 2003, pp. 397-9. doi : 10.1093 / nar / gkg001 . PMID 12520032 . PMC 165448 (free full text).

[pmid14990451-26] Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R: Predicting Subcellular localization of proteins using machine-learned classifier . In: Bioinformatics . 20, No. 4, March 2004, pp. 547-56. PMID 14990451 .

[pmid21873639-27] Mooney C, Wang YH, Pollastri G .: SCLpred: protein subcellular localization prediction by N-to-1 neural networks. . In: Bioinformatics . 27, No. 20, October 2011, pp. 2812-9. doi : 10.1093 / bioinformatics / btr494 . PMID 21873639 .

[pmid15115854-28] Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S: Feature-based prediction of non-classical and leaderless protein secretion . In: Protein Eng. Of. Sel. . 17, No. 4, April 2004, pp. 349-56. doi : 10.1093 / protein / gzh037 . PMID 15115854 .

[pmid17392328-29] Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O: SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data . In: Bioinformatics . 23, No. 11, June 2007, pp. 1410-7. doi : 10.1093 / bioinformatics / btm115 . PMID 17392328 .

[pmid10891285-30] Emanuelsson O, Nielsen H, Brunak S, von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence . In: J. Mol. Biol. . 300, No. 4, July 2000, pp. 1005-1016. doi : 10.1006 / jmbi.2000.3903 . PMID 10891285 .

[pmid17517783-31] Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K: WoLF PSORT: protein localization predictor . In: Nucleic Acids Res . 35, No. Web Server issue, July 2007, pp. W585-7. doi : 10.1093 / nar / gkm259 . PMID 17517783 . PMC 1933216 (free full text).

[pmid23982307-32] Saravanan V, Lakshmi PTV: APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein . In: Acta Biotheor . 61, No. 4, Dec 2013, pp. 481-497. doi : 10.1007 / s10441-013-9197-1 . PMID 23982307 .