Abstract
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.
We wish to thank Piotr Nowakowski for editorial work and Anna Śmietańska for technical support. Financial support for this research was provided by the Jagiellonian University Medical College grant system: K/ZDS/001531 and K/ZDS/002907. This project benefited from a PHC Polonium grant from Egide under no. 27748NE.
References
1. Nikolcheva T, Woodson SA. Facilitation of group I splicing in vivo: misfolding of the Tetrahymena IVS and the role of ribosomal RNA exons. J Mol Biol 1999;292:557–67.10.1006/jmbi.1999.3083Search in Google Scholar PubMed
2. Goux-Pelletan M, Libri D, d’Aubenton-Carafa Y, Fiszman M, Brody E, Marie J. In vitro splicing of mutually exclusive exons from the chicken β-tropomyosin gene: role of the branch point location and very long pyrimidine stretch. EMBO J 1990;9:241–9.10.1002/j.1460-2075.1990.tb08101.xSearch in Google Scholar PubMed PubMed Central
3. Ghosh DK, Rashid MB, Crane B, Taskar V, Mast M, Misukonis MA, et al. Characterization of key residues in the subdomain encoded by exons 8 and 9 of human inducible nitric oxide synthase: a critical role for Asp-280 in substrate binding and subunit interactions. Proc Natl Acad Sci USA 2001;98:10392–7.10.1073/pnas.181251298Search in Google Scholar PubMed PubMed Central
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;1793:281–9.10.1016/j.bbamcr.2008.09.012Search in Google Scholar PubMed PubMed Central
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.Search in Google Scholar
6. Panchenko AR, Madej T. Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins 2004;57:539–47.10.1002/prot.20237Search in Google Scholar PubMed PubMed Central
7. Madej T, Panchenko AR, Chen J, Bryant SH. Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar protein. BMC Struct Biol 2007;7:23.10.1186/1472-6807-7-23Search in Google Scholar PubMed PubMed Central
8. Thompson KE, Wang Y, Madej T, Bryant SH. Improving protein structure similarity searches using domain boundaries based on conserved sequence information. BMC Struct Biol 2009;9:33.10.1186/1472-6807-9-33Search in Google Scholar PubMed PubMed Central
9. Pintar A, Guarnaccia C, Dhir S, Pongor S. Exon 6 of human JAG1 encodes a conserved structural unit. BMC Struct Biol 2009;9:43.10.1186/1472-6807-9-43Search in Google Scholar PubMed PubMed Central
10. Greenfield NJ, Kotlyanskaya L, Hitchcock-DeGregori SE. Structure of the N terminus of a nonmuscle α-tropomyosin in complex with the C terminus: implications for actin binding. Biochemistry 2009;48:1272–83.10.1021/bi801861kSearch in Google Scholar PubMed PubMed Central
11. Pillmann H, Hatje K, Odronitz F, Hammesfahr B, Kollmar M. Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology. BMC Bioinform 2011;12:270.10.1186/1471-2105-12-270Search in Google Scholar PubMed PubMed Central
12. Chen L, Zheng S. Identify alternative splicing events based on position-specific evolutionary conservation. PLoS One 2008;3:e2806.10.1371/journal.pone.0002806Search in Google Scholar
13. Gelfman S, Burstein D, Penn O, Savchenko A, Amit M, Schwartz S, et al. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res 2012;22:35–50.10.1101/gr.119834.110Search in Google Scholar
14. Dhami P, Saffrey P, Bruce AW, Dillon SC, Chiang K, Bonhoure N, et al. Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution. PLoS One 2010;5:e12339.10.1371/journal.pone.0012339Search in Google Scholar
15. Konieczny L, Bryliński M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:589–600.Search in Google Scholar
16. Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976;104: 59–107.10.1016/0022-2836(76)90004-8Search in Google Scholar
17. Brylinski M, Konieczny L, Roterman I. Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl 2007;3:234–60.10.1504/IJBRA.2007.013605Search in Google Scholar
18. Kullback S, Leibler RA. On information and sufficiency. Ann Math Statist 1951;22:79–86.10.1214/aoms/1177729694Search in Google Scholar
19. Berezovsky I, Kirzhner V, Kirzhner A, Rosenfeld V, Trifonov E. Closed loops: persistence of the protein chain returns. Prot Eng 2003;15:955–7.10.1093/protein/15.12.955Search in Google Scholar
20. Berezovsky IN, Grosberg AY, Trifonov EN. Closed loops of nearly standard size: common basic element of protein structure. FEBS Lett 2000;466:283–6.10.1016/S0014-5793(00)01091-7Search in Google Scholar
21. Chintapalli SV, Yew BK, Illingworth CJ, Upton GJ, Reeves PJ, Parkes KE, et al. Closed loop folding units from structural alignments: experimental foldons revisited. J Comput Chem 2010;31:2689–701.10.1002/jcc.21562Search in Google Scholar PubMed
22. Lamarine M, Mornon JP, Berezovsky IN, Chomilier J. Distribution of tightened end fragments of globular proteins statistically match that of topohydrophobic positions: towards an efficient punctuation of protein folding? Cell Mol Life Sci 2001;58:492–8.10.1007/PL00000873Search in Google Scholar PubMed
23. Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 1996;3:842–8.10.1038/nsb1096-842Search in Google Scholar
24. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105–32.10.1016/0022-2836(82)90515-0Search in Google Scholar
25. Kim J, Nam KY, Cho KH, Choi SH, Noh JS, No KT. Theoretical study on hydrophobicity of amino acids by the solvation free energy density model. Bull Korean Chem Soc 2003;24:1742–50.10.5012/bkcs.2003.24.12.1742Search in Google Scholar
26. Janin J. Surface and inside volumes in globular proteins. Nature 1979;277:491–2.10.1038/277491a0Search in Google Scholar
27. Momany FA, McGuire RF, Burgess AW, Scheraga HA. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J Phys Chem 1974;79:2361–81.10.1021/j100589a006Search in Google Scholar
28. Panchenko A, Luthey-Shulten Z, Wolynes P. Foldons, protein structural modules, and exons. Proc Natl Acad Sci USA 1996;93:2008–13.10.1073/pnas.93.5.2008Search in Google Scholar
29. Yew B, Chintapalli S, Upton G, Reynolds C. Conservation of closed loops. J Mol Graph Model 2007;26:652–5.10.1016/j.jmgm.2007.03.011Search in Google Scholar
30. de Souza SJ, Long M, Schoenbach, L, Roy SW, Gilbert W. Intron positions correlate with module boundaries in ancient proteins. Proc Natl Acad Sci USA 1996;93:14632–6.10.1073/pnas.93.25.14632Search in Google Scholar
31. de Souza SJ, Long M, Schoenbach L, Roy SW, Gilbert W. The correlation between introns and the three dimensional structure of proteins. Gene 1997;205:141–4.10.1016/S0378-1119(97)00401-0Search in Google Scholar
32. Piwowar M, Banach M, Konieczny L, Roterman I. Structural role of exon-coded fragments in proteins. Int J Mol Sci, in press.Search in Google Scholar
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.Search in Google Scholar
34. Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1–63.10.1016/S0065-3233(08)60608-7Search in Google Scholar
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;18:229–37.10.1007/s00894-011-1033-4Search in Google Scholar PubMed PubMed Central
36. Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol 2011;283:60–70.10.1016/j.jtbi.2011.05.027Search in Google Scholar PubMed
37. Brylinski M, Konieczny L, Roterman I. Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 2006;30:255–67.10.1016/j.compbiolchem.2006.04.007Search in Google Scholar PubMed
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: 519–28.10.1080/07391102.2006.10507076Search in Google Scholar PubMed
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;432:275–82.10.1042/BJ20100642Search in Google Scholar PubMed PubMed Central
40. Nasimuzzaman M, Khandros E, Wang X, Kong Y, Zhao H, Weiss D, et al. Analysis of α hemoglobin stabilizing protein overexpression in murine β-thalassemia. Am J Hematol 2010;85:820–2.10.1002/ajh.21829Search in Google Scholar PubMed PubMed Central
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;117:1856–65.10.1172/JCI31664Search in Google Scholar PubMed PubMed Central
42. Brillet T, Baudin-Creuza V, Vasseur C, Domingues-Hamdi ED, Kiger L, Wajcman H, et al. α-Hemoglobin stabilizing protein (AHSP), a kinetic scheme of the action of a human mutant, AHSPV56G. J Biol Chem 2010;285:17986–92.10.1074/jbc.M109.098491Search in Google Scholar PubMed PubMed Central
43. Strandberg B. Building the ground for the first two protein structures: myoglobin and haemoglobin. J Mol Biol 2009;392: 2–10.10.1016/j.jmb.2009.05.087Search in Google Scholar PubMed
44. Mollan TL, Yu X, Weiss MJ, Olson JS. The role of α-hemoglobin stabilizing protein in redox chemistry, denaturation, and hemoglobin assembly. Antioxid Redox Signal 2010;12:219–31.10.1089/ars.2009.2780Search in Google Scholar PubMed PubMed Central
45. Pesce A, Milani M, Nardini M, Bolognesi M. Mapping heme-ligand tunnels in group I truncated(2/2) hemoglobins. Methods Enzymol 2008;436:303–15.10.1016/S0076-6879(08)36017-0Search in Google Scholar
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;18:8–16.10.1016/j.jasms.2006.08.013Search in Google Scholar
47. Arata Y. Effect of the tertiary structure alteration by ligation on the interface contacts between subunits of hemoglobin. Biochim Biophys Acta 1995;1247:24–34.10.1016/0167-4838(94)00196-NSearch in Google Scholar
48. Franchi D, Fronticelli C, Bucci E. Folding domains as functional tools in allosteric systems: a heme-dependent domain in hemoglobin β subunits. Biochemistry 1982;21:6181–7.10.1021/bi00267a024Search in Google Scholar PubMed
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;287:11338–50.10.1074/jbc.M111.313247Search in Google Scholar PubMed PubMed Central
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;435:697–701.10.1038/nature03609Search in Google Scholar PubMed
51. Szolajska E, Chroboczek J. Faithful chaperones. Cell Mol Life Sci 2011;68:3307–22.10.1007/s00018-011-0740-4Search in Google Scholar PubMed PubMed Central
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;19:91–7.10.1093/protein/gzj006Search in Google Scholar PubMed
53. França GS, Cancherini DV, de Souza SJ. Evolutionary history of exon shuffling. Genetica 2012;140:249–57.10.1007/s10709-012-9676-3Search in Google Scholar PubMed
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;8:327–37.10.2478/bams-2012-0023Search in Google Scholar
55. Sałapa K, Kalinowska B, Jadczyk T, Roterman I. Measurement of hydrophobicity distribution in proteins – complete redundant Protein Data Bank. Bio-Algorithms Med-Syst 2012;8:195–206.10.2478/bams-2012-0018Search in Google Scholar
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