Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
Warianty tytułu
Języki publikacji
The presented results cover issues related to proteins that were “never born in nature”. The paper is focused on identifying genetic information stretches of protein sequences that were not identified to be existing in nature. The aim of the work was finding traces of “never born proteins” (NBP) everywhere in completely sequenced genomes including regions not expected as carrying the genetic information. The results of analyses relate to the search of the genetic material of species from different levels of the evolutionary tree from yeast through plant organisms up to the human genome. The analysis concerns searching the genome sequences. There are presented statistical details such as sequence frequencies, their length, percent identity and similarity of alignments, as well as E value of sequences found. Computations were performed on gLite-based grid environment. The results of the analyses showed that the NBP genetic record in the genomes of the studied organisms is absent at a significant level in terms of identity of contents and length of the sequences found. Most of the found sequences considered to be similar do not exceed 50% of the length of the NBP output sequences, which confirms that the genetic record of proteins is not accidental in terms of composition of gene sequences but also as regards the place of recording in genomes of living organisms.
Opis fizyczny
Bibliogr. 30 poz., rys., wykr.
  • Department of Bioinformatics and Telemedicine, Jagiellonian University – Collegium Medicum, Kopernika 7e, PL-31-034, Krakow, Poland, Phone/Fax: +48124227764
  • Institute of Computer Science, Jagiellonian University, Krakow, Poland
  • Department of Computer Science, AGH University of Science and Technology, Krakow, Poland
  • Academic Computer Center CYFRONET, AGH University of Science and Technology, Krakow, Poland
  • Department of Bioinformatics and Telemedicine, Jagiellonian University – Collegium Medicum, Kopernika 7e, PL-31-034, Krakow, Poland
  • 1. Szybalski W. In vivo and in vitro initiation of transcription. Adv Exp Med Biol 1974;44:23–4.
  • 2. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008;319:1215–20.
  • 3. Luisi PL, Chiarabelli C, Stano P. From never born proteins to minimal living cells: two projects in synthetic biology. Orig Life Evol Biosph 2006;36:605–16.
  • 4. De Lucrezia D, Franchi M, Chiarabelli C, Gallori E, Luisi PL. Investigation of de novo totally random biosequences, part III: RNA Foster: a novel assay to investigate RNA folding structural properties. Chem Biodivers 2006;3:860–8.
  • 5. Chiarabelli C, Vrijbloed JW, Thomas RM, Luisi PL. Investigation of de novo totally random biosequences, part I: a general method for in vitro selection of folded domains from a random polypeptide library displayed on phage. Chem Biodivers 2006;3:827–39.
  • 6. Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochanczyk M, Flis L, et al. Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 2008;3:177–9.
  • 7. Chessari S, Thomas R, Polticelli F, Luisi PL. The production of de novo folded proteins by a stepwise chain elongation: a model for prebiotic chemical evolution of macromolecular sequences. Chem Biodivers 2006;3:1202–10.
  • 8. Chiarabelli C, Stano P, Anella F, Carrara P, Luisi PL. Approaches to chemical synthetic biology. FEBS Lett 2012;586:2138–45.
  • 9. Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, et al. In silico structural study of random amino acid sequence proteins not present in nature. Chem Biodivers 2009;6:2311–36.
  • 10. Minervini G, Evangelista G, Villanova L, Slanzi D, De Lucrezia D, Poli I, et al. Massive non-natural proteins structure prediction using grid technologies. BMC Bioinform 2009;10:S22.
  • 11. Piwowar M, Banach M, Konieczny L, Roterman I. Hydrophobic core formation in protein complex of cathepsin. J Biomol Struct Dyn 2014;32:1023–32.
  • 12. Liu Y, Kuhlman B. RosettaDesign server for protein design. Nucleic Acids Res 2006;34:W235–8.
  • 13. Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, et al. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 2003;53:457–68.
  • 14. Malawski M, Szepieniec T, Kochanczyk M, Piwowar M, Roterman I. An approach to protein folding on the Grid – {EUChinaGRID} experience. Bio-Algorithms Med-Syst 2007;3:45–50.
  • 15. Prymula K, Piwowar M, Kochańczyk M, Flis Ł, Malawski M, Szepieniec T, et al. Large scale computing to search for pharmacologically active proteins. In: KU KDM 2010: third ACC Cyfronet AGH users, 2010:12–3.
  • 16. Chiarabelli C, Vrijbloed JW, De Lucrezia D, Thomas RM, Stano P, Polticelli F, et al. Investigation of de novo totally random biosequences, part II: on the folding frequency in a totally random library of de novo proteins obtained by phage display. Chem Biodivers 2006;3:840–59.
  • 17. Jurkowski W, Brylinski M, Konieczny L, Roterman I. Lysozyme folded in silico according to the limited conformational subspace. J Biomol Struct Dyn 2004;22:149–58.
  • 18. Brylinski M, Konieczny L, Roterman I. Fuzzy-oil-drop hydrophobic force field – a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dyn 2006;23:519–28.
  • 19. Altschul SF, Gish W, Miller W, Myers, EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–10.
  • 20. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997;268:78–94.
  • 21. Stadie H, Ernst M, Ferrando J, Mankel R, Wrona K. Monte Carlo mass production for the ZEUS experiment on the grid. Nucl Instrum Meth A 2006;559:43–47.
  • 22. R Core Team. R: a language and environment for statistical computing. Vienna, Austria 2015.
  • 23. Peregrin-Alvarez JM, Parkinson J. The global landscape of sequence diversity. Genome Biol 2007;8:R238.
  • 24. Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014;5:399–412.
  • 25. Kryukov K, Sumiyama K, Ikeo K, Gojobori T, Saitou N. A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses. Genome Biol Evol 2012;4:501–12.
  • 26. Craig JM, Bickmore WA. The distribution of CpG islands in mammalian chromosomes. Nat Genet 1994;7:376–82.
  • 27. Gardiner K. Human genome organization. Curr Opin Genet Dev 1995;5:315–22.
  • 28. Bernardi G. The vertebrate genome: isochores and evolution. Mol Biol Evol 1993;10:186–204.
  • 29. Piwowar M, Meus J, Piwowar P, Wiśniowski Z, Stefaniak J, Roterman I. Tandemly repeated trinucleotides – comparative analysis. Acta Biochim Pol 2006;53:279–287.
  • 30. Ulmschneider MB, Sansom MS. Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta Biomembr 2001;1512:1–14.
Typ dokumentu
Identyfikator YADDA
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.