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Genetic traces of never born proteins

Identyfikatory
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
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.
Rocznik
Strony
79--87
Opis fizyczny
Bibliogr. 30 poz., rys., wykr.
Twórcy
autor
  • 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
autor
  • 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
Bibliografia
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-9fca3b78-038d-4871-94d1-18cd237963f1
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