PROTEOMIC TECHNOLOGIES AND DEVELOPMENT BIOINFORMATION RESOURCES
Abstract
In a review modern data on proteomic and bioinformation technologies of development of biochemistry of proteins are presented. It is shown that the coding capacity of matrix DNA cannot provide completely mitochondria’s in proteins. Data that there are five various mechanisms of import of proteins in a mitochondrion are given. Data that there are restrictions of computing technologies which consist in big percent of the false positive results, and also in impossibility of detection of target-signals for everything proteom are given. Advantages of tandem mass spectrometry to carrying out such researches are shown. Also, on localization of proteins it is possible to carry microscopy methods at which the principle of immunofluorescence of nature proteins is used to successfully applied approaches. Data on the main properties of proteoms proteins are provided.
Keywords
матричная ДНК,
белки,
митохондрии,
протеомы,
диагностика,
matrix DNA,
proteins,
mitochondrions,
proteoms,
diagnostics
About the Authors
T. . Snisarenko
Moscow State Regional University
Russian Federation
Russian Federation
R. . Rasulov
State Scientific Center of the Russian Federation, Federal State Unitary Enterprise «State Scientific Research Institute of Chemistry and Technology of Organoelement Compounds»
Russian Federation
Russian Federation
M. . Susova
State Scientific Center of the Russian Federation, Federal State Unitary Enterprise «State Scientific Research Institute of Chemistry and Technology of Organoelement Compounds»
Russian Federation
Russian Federation
M. . Rasulov
State Scientific Center of the Russian Federation, Federal State Unitary Enterprise «State Scientific Research Institute of Chemistry and Technology of Organoelement Compounds»
Russian Federation
Russian Federation
References
1. Примроуз С., Тваймен Р. Геномика: роль в медицине. - М.: Бином. Лаборатория знаний, 2008. - 277 с.
2. Adachi J. In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics / J. Adachi, C. Kumar, Y. Zhang et al. // Mol. Cell Proteomics. - 2007. - V. 6. - P. 1257-1273.
3. de Almeida A.M., Bendixen E. Pig proteomics: a review of a species in the crossroad between biomedical and food sciences // J. Proteomics. - 2012. - V. 75 (№ 14). - P. 4296-4314.
4. Anderson N.G., Matheson A., Anderson N.L. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology // Proteomics. -2001. - V. 1 (№ 1). - Р. 3-12.
5. Banci L. MIA40 is an oxidoreductase that catalyzes oxidative protein folding in mitochondria / L. Banci, I. Bertini, C. Cefaro et al. // Nat. Struct. Mol. Biol. - 2009. - V. 16. - P. 198-206.
6. Brustovetsky N., Dubinsky J.M. Dual ISSN 2072-8352 j Вестник МГОУ. Серия «Естественные науки» f 2014 / № 2 responses of CNS mitochondria to elevated calcium // J. Neurosci. - 2000. - V. 20 (№ 1). - P. 103-113.
7. Chacinska A. Importing mitochondrial proteins: machineries and mechanisms / A. Chacinska, C.M. Koehler, D. Milenkovic et al. // Cell. - 2009. - V. 138. - P. 628-644.
8. Chou A.P. Mechanisms of rotenone-induced proteasome inhibition / A.P. Chou, S. Li, A.G. Fitzmaurice et al. // Neurotoxicology. - 2010. - V. 31 (№ 4). -P. 367-372.
9. Costa C. Electrophysiology and pharmacology of striatal neuronal dysfunction induced by mitochondrial complex I inhibition / C. Costa, V. Belcastro, A. Tozzi et al. // J. Neurosci. - 2008. - V. 28 (№ 32). - P. 8040-52.
10. David F.P., Yip Y.L. SSMap: a new Uni-Prot-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase // BMC Bioinformatics. - 2008. - 9: 391. - 12 р.
11. DiMauro S., Davidzon G. Mitochondrial DNA and disease // Ann. Med. - 2005. -V. 37. - P. 222-232.
12. DiMauro S., Schon E.A. Mitochondrial respiratory-chain diseases // N. Engl. J. Med. - V. 348 (№ 26). - P. 2656-2668.
13. Falkenberg M. Mitochondrial transcription factors B1 and B2 activate transcription of human mtDNA / M. Falkenberg, M. Gaspari, A. Rantanen et al. // Nat. Genet. - 2002. - V. 31 (№ 3). - P. 289-294.
14. Fernandez-Vizarra E. Tissue-specific differences in mitochondrial activity and biogenesis / E. Fernandez-Vizarra, J.A. Enriquez, A. Pérez-Martos et al. // Mitochondrion. - 2011. - V. 11 (№ 1). - P. 207-213.
15. Foster L.J. A mammalian organelle map by protein correlation profiling / L.J. Foster, C.L. de Hoog, Y. Zhang et al. // Cell. - 2006. - 125. - Р. 187-199.
16. Forner F. Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver / F. Forner, L.J. Foster, S. Campanaro et al. // Mol. Cell Proteomics. - 2006. - V. 5. - Р. 608-619.
17. Gleyzer N., Vercauteren K., Scarpulla R.C. Control of mitochondrial transcription specificity factors (TFB1M and TFB2M) by nuclear respiratory factors (NRF-1 and NRF-2) and PGC-1 family coactivators // Mol. Cell. Biol. - 2005. -V. 25 (№ 4). - P. 1354-1366.
18. Gordon J.W. Effects of contractile activity on mitochondrial transcription factor A expression in skeletal muscle // J. Appl. Physiol. - 2001. - V. 90 (№ 1). - P. 389-396.
19. Huh W.K. Global analysis of protein localization in budding yeast / W.K. Huh, J.V. Falvo, C.L. Gerke et al. // Nature. - 2003. - V. 425. - P. 686-691.
20. Human physiology / ed. R.F. Schmidt, G. Thews G. - 2-nd ed. - New York: Springer, 2001. - 643 p.
21. Jänsch L. Unique composition of the preprotein translocase of the outer mitochondrial membrane from plants / L. Jänsch, V. Kruft, U.K. Schmitz et al. // J. Biol. Chem. - 1998. - V. 273 (№ 27). - P. 17251-7.
22. Johnson D.T. Functional consequences of mitochondrial proteome heterogeneity / D.T. Johnson, R.A. Harris, P.V. Blair et al. // Am. J. Physiol. Cell Physiol. - 2007. - V. 292. - P. 698-707.
23. Johnson D.T. Tissue heterogeneity of the mammalian mitochondrial proteome / D.T. Johnson, R.A. Harris, S. French et al. // Am. J. Physiol. Cell Physiol. - 2007. - V. 292. - P. 689-697.
24. Kilbride S.M. Partial inhibition of complex I activity increases Ca-independent glutamate release rates from depolarized synaptosomes / S.M. Kilbride, J.E. Telford, K.F. Tipton et al. // Neurochem. - 2008. - V. 106 (№ 2). - P. 826-834.
25. Kislinger T. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling / T. Kislinger, B. Cox, A. Kannan et al. // Cell. - 2006. - V. 125. - P. 173-186.
26. Kumar A. Subcellular localization of the yeast proteome / A. Kumar, S. Agarwal, J.A. Heyman et al. // Genes Dev. - 2002. -V. 16. - P. 707-719.
27. Larsson N.G. Mitochondrial transcription factor A is necessary for mtDNA maintenance and embryogenesis in mice / N.G. Larsson, J. Wang, H. Wilhelmsson et al. // Nat. Genet. - 1998. - V. 18 (№ 3). - P. 231-236.
28. Longley M.J. The fidelity of human DNA polymerase gamma with and without ex-onucleolytic proofreading and the p55 accessory subunit // J. Biol. Chem. - 2001. -V. 276 (№ 42). - 38555-62.
29. Lopez M.F. High-throughput pro- filing of the mitochondrial proteome using affinity fractionation and automation / M.F. Lopez, B.S. Kristal, E. Chernokalskaya et al. // Electrophoresis. - 2000. - V. 21. - 3427-40.
30. MacKenzie J.A., Payne R.M. Mitochondrial Protein Import and Human Health and Disease // Biochim. Biophys. Acta. -2007. - № 5. - P. 509-523.
31. McCulloch V., Seidel-Rogol B.L., Shadel G.S. A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine // Mol. Cell. Biol. - 2002. - V. 22. - P. 1116-1125.
32. Milenkovic D. Identification of the signal directing Tim9 and Tim10 into the intermembrane space of mitochondria / D. Milenkovic, T. Ramming, J.M. Muller, et al. // Mol. Biol. Cell. - 2009. - 20: 2530-39.
33. Miyadera H. Atpenins, potent and specific inhibitors of mitochondrial complex II (succinate-ubiquinone oxidoreductase) / H. Miyadera, K. Shiomi, H. Ui et al. // Proc. Natl. Acad. Sci. USA. - 2003. - V. 100. -P. 473-477.
34. Mootha V.K. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria / V.K. Mootha, J. Bunkenborg, J.V. Olsen et al. // Cell. - 2003. - V. 115. - Р. 629-640.
35. Nicholls D.G. Forty years of Mitchell’s proton circuit: From little grey books to littlegrey cells // Biochim. Biophys. Acta. - 2008. - V. 1777. - P. 550-556.
36. Principe S. Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine / S. Principe, Y. Kim, S. Fontana et al. // J. Proteome Res. - 2012. - V. 11 (№ 4). - P. 2386-2396.
37. Rajapakse N. Isolation and characterization of intact mitochondria from neonatal rat brain / N. Rajapakse, K. Shimizu, M. Payne et al. // Brain Res. Protoc. - 2001. - V. 8 (№ 3). - P. 176-183.
38. Ruiz-Pesini E. An enhanced MITOMAP with a global mtDNA mutational phylogeny / E. Ruiz-Pesini, M.T. Lott, V. Procaccio et al. // Nucleic Acids Res. - 2007. - V. 35. - Р. 823-828.
39. Sun F. Crystal structure of mitochondrial respiratory membrane protein complex II / F. Sun, X. Huo, Y. Zhai et al. // Cell. -2005. - V. 121. - P. 1043-1057.
40. Takamatsu C. Regulation of mitochondrial D-loops by transcription factor A and single-stranded DNA-binding protein / C. Takamatsu, S. Umeda, T. Ohsato et al. // EMBO Rep. - 2002. - V. 3 (№ 5). - P. 451-456.
41. Taylor S.W. Characterization of the human heart mitochondrial proteome / S.W. Taylor, E. Fahy, B. Zhang et al. // Nat. Biotechnol. - 2003. - V. 21. - P. 281-286.
42. Taylor R.W. Molecular basis for treatment of mitochondrial myopathies / R.W. Taylor, T.M. Wardell, R.N. Lightowlers et al. // Neurol. Sci. - 2000. - V. 21. - P. 909-912.
43. Theodossiou T.A. Papakyriakou A., Hothersall J.S. Molecular modeling and experimental evidence for hypericin as a substrate for mitochondrial complex III; mitochondrial photodamage as demonstrated using specific inhibitors // Free Radic. Biol. Med. - 2008. - V. 45 (№ 11). - P. 1581-1590.
44. Thiele I. Candidate metabolic network states in human mitochondria / I. Thiele, ISSN 2072-8352 j Вестник МГОУ. Серия «Естественные науки» f 2014 / № 2 N.D. Price, T.D. Vo et al. // J. Biol. Chem. [Impact of diabetes, ischemia, and diet]. -2005. - V. 280. - 11683-95.
45. Vo T.D., Greenberg H.J., Palsson B.O. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data // J. Biol. Chem. - 2004. - V. 279. - 39532-40.
46. Wharton D.C., Tzagoloff A. Cytochrome oxidase from beef heart mitochondria. Methods Enzymol. - 1967. - V. 10. - P. 245-250.
47. Yip Y.L. Annotating single amino acid polymorphisms in the UniProt/SwissProt knowledgebase / Y.L. Yip, M. Famiglietti, A. Gos et al. // Hum. Mutat. - 2008. - V. 29 (№ 3). - P. 361-366.
48. Zapata I., Zerby H.N., Wick M. Functional proteomic analysis predicts beef tenderness and the tenderness differential // J. Agric. Food Chem. - 2009. - V. 10. - V. 57 (№ 11). - P. 4956-63.
Review
Views:
128
Email this article 