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Abstrakty
EN
The role of exons can be studied on many levels, one of which pertains to protein structure. It is a well-known fact that secondary structural motifs do not directly correspond to exons: helices, β-sheets and loops have all been identified as encoded by more than one exon. The relation between exon fragments and their involvement in shaping the three-dimensional (3D) structure of a protein body is subject to ongoing studies. In particular, the role of exons in stabilizing tertiary structures can be related to the structure of the hydrophobic core of the protein. Participation of specific polypeptide fragments (single exons) in hydrophobic stabilization reveals the role played by each fragment. In the course of the presented research, exons in selected proteins have been identified on the basis of GenBank files, imported from the nucleotide database at the National Center of Biotechnology Information. Amino acid sequences representing each exon were subsequently traced to parts of 3D structural forms. The participation of each exon fragment in shaping the hydrophobic core of the protein was measured using divergence entropy calculations. It was found that each protein contains at least one exon which encodes a structural fragment in accordance with the theoretical hydrophobic core model. This implies that the likely role of at least one exon in each protein is to generate a hydrophobic core which is, in turn, responsible for tertiary structural stabilization.
Słowa kluczowe
Rocznik
Strony
81--90
Opis fizyczny
Bibliogr. 55 poz., rys.
Twórcy
autor
  • Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Kraków, Poland
autor
  • Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Kraków, Poland
  • Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
autor
  • Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland
autor
  • IMPMC, Université Pierre et Marie Curie, CNRS, 4 Place Jussieu, Paris, France
  • RPBS, 35 rue Hélène Brion, Paris, France
autor
  • Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Kraków, Poland
Bibliografia
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  • 4. Seo P-S, Jeong JJ, Zeng L, Takoudis CG, Quinn BJ, Khan AA, et al. Alternatively spliced exon 5 of the FERM domain of Protein 4.1R encodes a novel binding site for erythrocyte p55 and is critical for membrane targeting in epithelial cells. Biochim Biophys Acta 2009;1793:281–9.
  • 5. Jin Xu J, Xu M, Rossi GC, Pasternak GW, Pan Y-X. Identification and characterization of seven new exon 11-associated splice variants of the rat μ opioid receptor gene, OPRM1. Mol Pain 2011;7:9.
  • 6. Panchenko AR, Madej T. Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins 2004;57:539–47.
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  • 33. Banach M, Marchewka M, Piwowar M, Roterman I. Divergence entropy characterizing the internal force field in proteins. In: Roterman-Konieczna I, editor. Protein folding in silico: protein folding versus protein structure prediction. Woodhead, 2012.
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  • 35. Banach M, Prymula K, Jurkowski W, Konieczny L, Roterman I. Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. J Mol Model 2012;18:229–37.
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  • 37. Brylinski M, Konieczny L, Roterman I. Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 2006;30:255–67.
  • 38. 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.
  • 39. Krishna Kumar K, Dickson CF, Weiss MJ, Mackay JP, Gell DA. AHSP (α-haemoglobin-stabilizing protein) stabilizes apo-α-haemoglobin in a partially folded state. Biochem J 2010;432:275–82.
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  • 41. Yu X, Kong Y, Dore LC, Abdulmalik O, Katein AM, Zhou S, et al. An erythroid chaperone that facilitates folding of α-globin subunits for hemoglobin synthesis. J Clin Invest 2007;117:1856–65.
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  • 45. Pesce A, Milani M, Nardini M, Bolognesi M. Mapping heme-ligand tunnels in group I truncated(2/2) hemoglobins. Methods Enzymol 2008;436:303–15.
  • 46. Boys BL, Konermann L. Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system. J Am Soc Mass Spectrom 2007;18:8–16.
  • 47. Arata Y. Effect of the tertiary structure alteration by ligation on the interface contacts between subunits of hemoglobin. Biochim Biophys Acta 1995;1247:24–34.
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  • 49. Mollan TL, Khandros E, Weiss MJ, Olson JS. Kinetics of α-globin binding to α-hemoglobin stabilizing protein (AHSP) indicate preferential stabilization of hemichrome folding intermediate. J Biol Chem 2012;287:11338–50.
  • 50. Feng L, Zhou S, Gu L, Gell DA, Mackay JP, Weiss MJ, et al. Structure of oxidized α-haemoglobin bound to AHSP reveals a protective mechanism for haem. Nature 2005;435:697–701.
  • 51. Szolajska E, Chroboczek J. Faithful chaperones. Cell Mol Life Sci 2011;68:3307–22.
  • 52. Vasseur-Godbillon C, Hamdane D, Marden MC, Baudin-Creuza V. High-yield expression in Escherichia coli of soluble human α-hemoglobin complexed with its molecular chaperone. Prot Eng 2006;19:91–7.
  • 53. França GS, Cancherini DV, de Souza SJ. Evolutionary history of exon shuffling. Genetica 2012;140:249–57.
  • 54. Sałapa K, Kalinowska B, Jadczyk T, Roterman I. Measurement of hydrophobicity distribution in proteins – non-redundant Protein Data Bank. Bio-Algorithms Med-Syst 2012;8:327–37.
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Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-9d88127f-29a4-4dc2-b0cd-4411e734b111
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