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. 2002 Sep;83(3):1268–1280. doi: 10.1016/S0006-3495(02)73899-X

Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments.

R I Dima 1, D Thirumalai 1
PMCID: PMC1302227  PMID: 12202354

Abstract

Neurodegenerative diseases induced by transmissible spongiform encephalopathies are associated with prions. The most spectacular event in the formation of the infectious scrapie form, referred to as PrP(Sc), is the conformational change from the predominantly alpha-helical conformation of PrP(C) to the PrP(Sc) state that is rich in beta-sheet content. Using sequence alignments and structural analysis of the available nuclear magnetic resonance structures of PrP(C), we explore the propensities of helices in PrP(C) to be in a beta-strand conformation. Comparison of a number of structural characteristics (such as solvent accessible area, distribution of (Phi, Psi) angles, mismatches in hydrogen bonds, nature of residues in local and nonlocal contacts, distribution of regular densities of amino acids, clustering of hydrophobic and hydrophilic residues in helices) between PrP(C) structures and a databank of "normal" proteins shows that the most unusual features are found in helix 2 (H2) (residues 172-194) followed by helix 1 (H1) (residues 144-153). In particular, the C-terminal residues in H2 are frustrated in their helical state. The databank of normal proteins consists of 58 helical proteins, 36 alpha+beta proteins, and 31 beta-sheet proteins. Our conclusions are also substantiated by gapless threading calculations that show that the normalized Z-scores of prion proteins are similar to those of other alpha+beta proteins with low helical content. Application of the recently introduced notion of discordance, namely, incompatibility of the predicted and observed secondary structures, also points to the frustration of H2 not only in the wild type but also in mutants of human PrP(C). This suggests that the instability of PrP(C) proteins may play a role in their being susceptible to the profound conformational change. Our analysis shows that, in addition to the previously proposed role for the segment (90-120) and possibly H1, the C-terminus of H2 and possibly N-terminus may play a role in the alpha-->beta transition. An implication of our results is that the ease of polymerization depends on the unfolding rate of the monomer. Sequence alignments show that helices in avian prion proteins (chicken, duck, crane) are better accommodated in a helical state, which might explain the absence of PrP(Sc) formation over finite time scales in these species. From this analysis, we predict that correlated mutations that reduce the frustration in the second half of helix 2 in mammalian prion proteins could inhibit the formation of PrP(Sc).

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aurora R., Rose G. D. Helix capping. Protein Sci. 1998 Jan;7(1):21–38. doi: 10.1002/pro.5560070103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baskakov I. V., Legname G., Prusiner S. B., Cohen F. E. Folding of prion protein to its native alpha-helical conformation is under kinetic control. J Biol Chem. 2001 Apr 16;276(23):19687–19690. doi: 10.1074/jbc.C100180200. [DOI] [PubMed] [Google Scholar]
  3. Baud F., Karlin S. Measures of residue density in protein structures. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12494–12499. doi: 10.1073/pnas.96.22.12494. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235–242. doi: 10.1093/nar/28.1.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Billeter M., Riek R., Wider G., Hornemann S., Glockshuber R., Wüthrich K. Prion protein NMR structure and species barrier for prion diseases. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7281–7285. doi: 10.1073/pnas.94.14.7281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
  7. Caughey B. W., Dong A., Bhat K. S., Ernst D., Hayes S. F., Caughey W. S. Secondary structure analysis of the scrapie-associated protein PrP 27-30 in water by infrared spectroscopy. Biochemistry. 1991 Aug 6;30(31):7672–7680. doi: 10.1021/bi00245a003. [DOI] [PubMed] [Google Scholar]
  8. Chan C. K., Hu Y., Takahashi S., Rousseau D. L., Eaton W. A., Hofrichter J. Submillisecond protein folding kinetics studied by ultrarapid mixing. Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1779–1784. doi: 10.1073/pnas.94.5.1779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chou P. Y., Fasman G. D. Empirical predictions of protein conformation. Annu Rev Biochem. 1978;47:251–276. doi: 10.1146/annurev.bi.47.070178.001343. [DOI] [PubMed] [Google Scholar]
  10. Cohen F. E., Pan K. M., Huang Z., Baldwin M., Fletterick R. J., Prusiner S. B. Structural clues to prion replication. Science. 1994 Apr 22;264(5158):530–531. doi: 10.1126/science.7909169. [DOI] [PubMed] [Google Scholar]
  11. Cohen F. E. Protein misfolding and prion diseases. J Mol Biol. 1999 Oct 22;293(2):313–320. doi: 10.1006/jmbi.1999.2990. [DOI] [PubMed] [Google Scholar]
  12. Cohen F. E., Prusiner S. B. Pathologic conformations of prion proteins. Annu Rev Biochem. 1998;67:793–819. doi: 10.1146/annurev.biochem.67.1.793. [DOI] [PubMed] [Google Scholar]
  13. Donne D. G., Viles J. H., Groth D., Mehlhorn I., James T. L., Cohen F. E., Prusiner S. B., Wright P. E., Dyson H. J. Structure of the recombinant full-length hamster prion protein PrP(29-231): the N terminus is highly flexible. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13452–13457. doi: 10.1073/pnas.94.25.13452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gasset M., Baldwin M. A., Fletterick R. J., Prusiner S. B. Perturbation of the secondary structure of the scrapie prion protein under conditions that alter infectivity. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):1–5. doi: 10.1073/pnas.90.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hooft R. W., Vriend G., Sander C., Abola E. E. Errors in protein structures. Nature. 1996 May 23;381(6580):272–272. doi: 10.1038/381272a0. [DOI] [PubMed] [Google Scholar]
  16. Hornemann S., Glockshuber R. A scrapie-like unfolding intermediate of the prion protein domain PrP(121-231) induced by acidic pH. Proc Natl Acad Sci U S A. 1998 May 26;95(11):6010–6014. doi: 10.1073/pnas.95.11.6010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hosszu L. L., Baxter N. J., Jackson G. S., Power A., Clarke A. R., Waltho J. P., Craven C. J., Collinge J. Structural mobility of the human prion protein probed by backbone hydrogen exchange. Nat Struct Biol. 1999 Aug;6(8):740–743. doi: 10.1038/11507. [DOI] [PubMed] [Google Scholar]
  18. Istrail S., Schwartz R., King J. Lattice simulations of aggregation funnels for protein folding. J Comput Biol. 1999 Summer;6(2):143–162. doi: 10.1089/cmb.1999.6.143. [DOI] [PubMed] [Google Scholar]
  19. James T. L., Liu H., Ulyanov N. B., Farr-Jones S., Zhang H., Donne D. G., Kaneko K., Groth D., Mehlhorn I., Prusiner S. B. Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform. Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10086–10091. doi: 10.1073/pnas.94.19.10086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kallberg Y., Gustafsson M., Persson B., Thyberg J., Johansson J. Prediction of amyloid fibril-forming proteins. J Biol Chem. 2000 Dec 27;276(16):12945–12950. doi: 10.1074/jbc.M010402200. [DOI] [PubMed] [Google Scholar]
  21. Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
  22. Liemann S., Glockshuber R. Influence of amino acid substitutions related to inherited human prion diseases on the thermodynamic stability of the cellular prion protein. Biochemistry. 1999 Mar 16;38(11):3258–3267. doi: 10.1021/bi982714g. [DOI] [PubMed] [Google Scholar]
  23. Lüthy R., Bowie J. U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992 Mar 5;356(6364):83–85. doi: 10.1038/356083a0. [DOI] [PubMed] [Google Scholar]
  24. McDonald I. K., Thornton J. M. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994 May 20;238(5):777–793. doi: 10.1006/jmbi.1994.1334. [DOI] [PubMed] [Google Scholar]
  25. Michelitsch M. D., Weissman J. S. A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):11910–11915. doi: 10.1073/pnas.97.22.11910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Morillas M., Vanik D. L., Surewicz W. K. On the mechanism of alpha-helix to beta-sheet transition in the recombinant prion protein. Biochemistry. 2001 Jun 12;40(23):6982–6987. doi: 10.1021/bi010232q. [DOI] [PubMed] [Google Scholar]
  27. Morrissey M. P., Shakhnovich E. I. Evidence for the role of PrP(C) helix 1 in the hydrophilic seeding of prion aggregates. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11293–11298. doi: 10.1073/pnas.96.20.11293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Murzin A. G., Brenner S. E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995 Apr 7;247(4):536–540. doi: 10.1006/jmbi.1995.0159. [DOI] [PubMed] [Google Scholar]
  29. Muñoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol. 1994 Jun;1(6):399–409. doi: 10.1038/nsb0694-399. [DOI] [PubMed] [Google Scholar]
  30. Orengo C. A., Michie A. D., Jones S., Jones D. T., Swindells M. B., Thornton J. M. CATH--a hierarchic classification of protein domain structures. Structure. 1997 Aug 15;5(8):1093–1108. doi: 10.1016/s0969-2126(97)00260-8. [DOI] [PubMed] [Google Scholar]
  31. Pan K. M., Baldwin M., Nguyen J., Gasset M., Serban A., Groth D., Mehlhorn I., Huang Z., Fletterick R. J., Cohen F. E. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):10962–10966. doi: 10.1073/pnas.90.23.10962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Peretz D., Williamson R. A., Matsunaga Y., Serban H., Pinilla C., Bastidas R. B., Rozenshteyn R., James T. L., Houghten R. A., Cohen F. E. A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. J Mol Biol. 1997 Oct 31;273(3):614–622. doi: 10.1006/jmbi.1997.1328. [DOI] [PubMed] [Google Scholar]
  33. Pergami P., Jaffe H., Safar J. Semipreparative chromatographic method to purify the normal cellular isoform of the prion protein in nondenatured form. Anal Biochem. 1996 Apr 5;236(1):63–73. doi: 10.1006/abio.1996.0132. [DOI] [PubMed] [Google Scholar]
  34. Prusiner S. B. Prion diseases and the BSE crisis. Science. 1997 Oct 10;278(5336):245–251. doi: 10.1126/science.278.5336.245. [DOI] [PubMed] [Google Scholar]
  35. Prusiner S. B. Prions. Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13363–13383. doi: 10.1073/pnas.95.23.13363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Riek R., Hornemann S., Wider G., Billeter M., Glockshuber R., Wüthrich K. NMR structure of the mouse prion protein domain PrP(121-231). Nature. 1996 Jul 11;382(6587):180–182. doi: 10.1038/382180a0. [DOI] [PubMed] [Google Scholar]
  37. Riek R., Hornemann S., Wider G., Glockshuber R., Wüthrich K. NMR characterization of the full-length recombinant murine prion protein, mPrP(23-231). FEBS Lett. 1997 Aug 18;413(2):282–288. doi: 10.1016/s0014-5793(97)00920-4. [DOI] [PubMed] [Google Scholar]
  38. Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584–599. doi: 10.1006/jmbi.1993.1413. [DOI] [PubMed] [Google Scholar]
  39. Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. doi: 10.1002/prot.340090107. [DOI] [PubMed] [Google Scholar]
  40. Simonic T., Duga S., Strumbo B., Asselta R., Ceciliani F., Ronchi S. cDNA cloning of turtle prion protein. FEBS Lett. 2000 Mar 3;469(1):33–38. doi: 10.1016/s0014-5793(00)01232-1. [DOI] [PubMed] [Google Scholar]
  41. Sparrer H. E., Santoso A., Szoka F. C., Jr, Weissman J. S. Evidence for the prion hypothesis: induction of the yeast [PSI+] factor by in vitro- converted Sup35 protein. Science. 2000 Jul 28;289(5479):595–599. doi: 10.1126/science.289.5479.595. [DOI] [PubMed] [Google Scholar]
  42. Srinivasan R., Rose G. D. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins. 1995 Jun;22(2):81–99. doi: 10.1002/prot.340220202. [DOI] [PubMed] [Google Scholar]
  43. Telling G. C., Scott M., Mastrianni J., Gabizon R., Torchia M., Cohen F. E., DeArmond S. J., Prusiner S. B. Prion propagation in mice expressing human and chimeric PrP transgenes implicates the interaction of cellular PrP with another protein. Cell. 1995 Oct 6;83(1):79–90. doi: 10.1016/0092-8674(95)90236-8. [DOI] [PubMed] [Google Scholar]
  44. Viles J. H., Donne D., Kroon G., Prusiner S. B., Cohen F. E., Dyson H. J., Wright P. E. Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry. 2001 Mar 6;40(9):2743–2753. doi: 10.1021/bi002898a. [DOI] [PubMed] [Google Scholar]
  45. Wildegger G., Liemann S., Glockshuber R. Extremely rapid folding of the C-terminal domain of the prion protein without kinetic intermediates. Nat Struct Biol. 1999 Jun;6(6):550–553. doi: 10.1038/9323. [DOI] [PubMed] [Google Scholar]
  46. Wille H., Zhang G. F., Baldwin M. A., Cohen F. E., Prusiner S. B. Separation of scrapie prion infectivity from PrP amyloid polymers. J Mol Biol. 1996 Jun 21;259(4):608–621. doi: 10.1006/jmbi.1996.0343. [DOI] [PubMed] [Google Scholar]
  47. Zahn R., Liu A., Lührs T., Riek R., von Schroetter C., López García F., Billeter M., Calzolai L., Wider G., Wüthrich K. NMR solution structure of the human prion protein. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):145–150. doi: 10.1073/pnas.97.1.145. [DOI] [PMC free article] [PubMed] [Google Scholar]

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