Prediction of Amyloid Fibril-forming Proteins

Abstract

In Alzheimer's disease and spongiform encephalopathies proteins transform from their native states into fibrils. We find that several amyloid-forming proteins harbor an α-helix in a polypeptide segment that should form a β-strand according to secondary structure predictions. In 1324 nonredundant protein structures, 37 β-strands with ≥7 residues were predicted in segments where the experimentally determined structures show helices. These discordances include the prion protein (helix 2, positions 179–191), the Alzheimer amyloid β-peptide (Aβ, positions 16–23), and lung surfactant protein C (SP-C, positions 12–27). In addition, human coagulation factor XIII (positions 258–266), triacylglycerol lipase from Candida antarctica (positions 256–266), andd-alanyl-d-alanine transpeptidase fromStreptomyces R61 (positions 92–106) contain a discordant helix. These proteins have not been reported to form fibrils but in this study were found to form fibrils in buffered saline at pH 7.4. By replacing valines in the discordant helical part of SP-C with leucines, an α-helix is found experimentally and by secondary structure predictions. This analogue does not form fibrils under conditions where SP-C forms abundant fibrils. Likewise, when Aβ residues 14–23 are removed or changed to a nondiscordant sequence, fibrils are no longer formed. We propose that α-helix/β-strand-discordant stretches are associated with amyloid fibril formation. In Alzheimer's disease and spongiform encephalopathies proteins transform from their native states into fibrils. We find that several amyloid-forming proteins harbor an α-helix in a polypeptide segment that should form a β-strand according to secondary structure predictions. In 1324 nonredundant protein structures, 37 β-strands with ≥7 residues were predicted in segments where the experimentally determined structures show helices. These discordances include the prion protein (helix 2, positions 179–191), the Alzheimer amyloid β-peptide (Aβ, positions 16–23), and lung surfactant protein C (SP-C, positions 12–27). In addition, human coagulation factor XIII (positions 258–266), triacylglycerol lipase from Candida antarctica (positions 256–266), andd-alanyl-d-alanine transpeptidase fromStreptomyces R61 (positions 92–106) contain a discordant helix. These proteins have not been reported to form fibrils but in this study were found to form fibrils in buffered saline at pH 7.4. By replacing valines in the discordant helical part of SP-C with leucines, an α-helix is found experimentally and by secondary structure predictions. This analogue does not form fibrils under conditions where SP-C forms abundant fibrils. Likewise, when Aβ residues 14–23 are removed or changed to a nondiscordant sequence, fibrils are no longer formed. We propose that α-helix/β-strand-discordant stretches are associated with amyloid fibril formation. Amyloid fibrils can be formed from different proteins and are associated with severe diseases like the neurodegenerative Alzheimer's disease and the prion diseases Creutzfeld-Jakob in humans, scrapie in sheep, and bovine spongiform encephalopathy, as well as other organ-specific and systemic amyloidoses (1Kelly J.W. Curr. Opin. Struct. Biol. 1996; 6: 11-17Crossref PubMed Scopus (568) Google Scholar). The ∼20 proteins that are associated with amyloid diseases have no obvious common properties in amino acid sequence, three-dimensional structure, or function (2Sipe J.D. Annu. Rev. Biochem. 1992; 61: 947-975Crossref PubMed Scopus (408) Google Scholar). Despite these differences in native structures, the amyloid fibrils are very similar irrespective from which protein they originate (3Dobson C.M. Trends Biochem. Sci. 1999; 24: 329-332Abstract Full Text Full Text PDF PubMed Scopus (1692) Google Scholar). Amyloid fibrils are built up from β-strands perpendicular and β-sheets parallel to the fiber axis (4Jiménez J.L. Guijarro J.I. Orlova E. Zurdo J. Dobson C.M. Sunde M. Saibil H.R. EMBO J. 1999; 18: 815-821Crossref PubMed Scopus (445) Google Scholar). Thus, amyloid-forming proteins that mainly contain α-helical structures in their native states must undergo α-helix → β-strand conversions before or during fibril formation. Tinctorial and spectroscopic studies indicate that the conversion of the cellular form of the prion protein (PrPC)1 to its fibrillar scrapie counterpart (PrPSc) is accompanied by reduction in α-helix content and increase in β-sheet structure (5Pan K.M. Baldwin M. Nguyen J. Gasset M. Serban A. Groth D. Mehlhorn I. Huang Z. Fletterick R.J. Cohen F.E. Prusiner S.B. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 10962-10966Crossref PubMed Scopus (2063) Google Scholar). Amyloid β-peptide (Aβ) fibril formation associated with Alzheimer's disease also involves α-helix to β-strand conversion (6Barrow C.J. Yasuda A. Kenny P.T. Zagorski M.G. J. Mol. Biol. 1992; 225: 1075-1093Crossref PubMed Scopus (607) Google Scholar). Amyloid diseases mostly occur without known precipitating factors (7Lansbury Jr., P.T. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 3342-3344Crossref PubMed Scopus (512) Google Scholar), and no explanation has yet been found to the occurrence ofde novo α → β conversion in amyloid-forming proteins. This conversion may occur in partially denaturing cellular environments (8Kelly J.W. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 930-932Crossref PubMed Scopus (117) Google Scholar), which, however, does not explain why only certain proteins form amyloid. Destabilizing point mutations can cause fibril formation of an otherwise stable protein (9Booth D.R. Sunde M. Bellotti V. Robinson C.V. Hutchinson W.L. Fraser P.E. Hawkins P.N. Dobson C.M. Radford S.E. Blake C.C.F. Pepys M.B. Nature. 1997; 385: 787-793Crossref PubMed Scopus (972) Google Scholar), but point mutations related to inherited forms of human prion diseases do not induce PrPSc in vitro and are not generally destabilizing (10Liemann S. Glockshuber R. Biochemistry. 1999; 38: 3258-3267Crossref PubMed Scopus (295) Google Scholar). The Aβ-(1–42)-peptide is highly fibrillogenic, whereas peptides lacking residues 14–23 are not (11Tjernberg L.O. Callaway D.J. Tjernberg A. Hahne S. Lilliehook C. Terenius L. Thyberg J. Nordstedt C. J. Biol. Chem. 1999; 274: 12619-12625Abstract Full Text Full Text PDF PubMed Scopus (330) Google Scholar). Proteins that give rise to amyloid may harbor polypeptide segments that make them more prone to undergo α → β conversions than nonamyloidogenic proteins. A key question is whether specific helices of these proteins are predisposed to undergo α → β conversions. Lung surfactant protein C (SP-C) is a 35-residue lipopeptide derived from a larger precursor by proteolysis. SP-C isolated from natural sources is composed of an α-helix covering positions 9–34 (12Johansson J. Szyperski T. Curstedt T. Wüthrich K. Biochemistry. 1994; 33: 6015-6023Crossref PubMed Scopus (176) Google Scholar). Monomeric α-helical SP-C is thermodynamically unstable, and the peptide irreversibly forms aggregates with β-sheet structure (13Szyperski T. Vandenbussche G. Curstedt T. Ruysschaert J.-M. Wüthrich K. Johansson J. Protein Sci. 1998; 7: 2533-2540Crossref PubMed Scopus (69) Google Scholar). SP-C assembles into amyloid fibrils upon incubation in solution, and fibrils composed of SP-C were isolated from a patient with the disease pulmonary alveolar proteinosis (14Gustafsson M. Thyberg J. Näslund J. Eliasson E. Johansson J. FEBS Lett. 1999; 464: 138-142Crossref PubMed Scopus (96) Google Scholar). The α-helix of mature SP-C contains a very long continuous stretch of valine residues, which is unusual since valines are well known to be overrepresented in β-strands and underrepresented in helices. Intriguingly, synthetic SP-C peptides are inefficient in helix formation but form insoluble aggregates (15Johansson J. Nilsson G. Strömberg R. Robertson B. Jörnvall H. Curstedt T. Biochem. J. 1995; 307: 535-541Crossref PubMed Scopus (87) Google Scholar). In contrast, peptides where the polyvaline segment of SP-C was replaced with a helical part of bacteriorhodopsin or a polyleucine stretch, both with high statistical helical propensities, readily form helices (15Johansson J. Nilsson G. Strömberg R. Robertson B. Jörnvall H. Curstedt T. Biochem. J. 1995; 307: 535-541Crossref PubMed Scopus (87) Google Scholar, 16Nilsson G. Gustafsson M. Vandenbussche G. Veldhuizen E. Griffiths W.J. Sjövall J. Haagsman H.P. Ruysschaert J.-M. Robertson B. Curstedt T. Johansson J. Eur. J. Biochem. 1998; 255: 116-124Crossref PubMed Scopus (84) Google Scholar). These features suggest that α-helices for which β-strands are predicted may be prone to undergo α-helix → β-strand transition and amyloid formation (14Gustafsson M. Thyberg J. Näslund J. Eliasson E. Johansson J. FEBS Lett. 1999; 464: 138-142Crossref PubMed Scopus (96) Google Scholar). Here we tested this hypothesis by searching for discrepancies between experimentally determined α-helices and predicted extended (β-strand) structures in 1324 nonredundant entries in the Protein Data Bank. This revealed a striking correlation between α/β discordance and ability to form amyloid fibrils. The May 1999 list of PDB_SELECT (17Hobohm U. Scharf M. Schneider R. Sander C. Protein Sci. 1992; 1: 409-417Crossref PubMed Scopus (774) Google Scholar) was initially used to obtain a nonhomologous set of proteins from the Brookhaven data base (18Berman H.M. Westbrook J. Feng Z. Gilliland G. Bhat T.N. Weissig H. Shindyalov I.N. Bourne P.E. Nucleic Acids Res. 2000; 28: 235-242Crossref PubMed Scopus (26946) Google Scholar). This list consists of 1106 sequences with less than 25% residue identity in pairwise comparisons. During the project a new version of PDB_SELECT was released (November 1999 set), and for completeness, proteins that were nonoverlapping with the May list were added to the data set. Using FASTA (19Pearson W.R. Lipman D.J. Proc. Natl. Acad. Sci. U. S. A. 1988; 85: 2444-2448Crossref PubMed Scopus (9362) Google Scholar), proteins in the November 1999 set that are not homologous to any of the proteins in the May set (expect value >0.1) were selected. This resulted in an addition of 218 proteins, and the final data set thus consisted of 1324 nonhomologous proteins. The secondary structure elements of the selected proteins were extracted from the Protein Data Bank files by Defined Secondary Structure of Proteins (20Kabsch W. Sander C. Biopolymers. 1983; 22: 2577-2637Crossref PubMed Scopus (12173) Google Scholar), as implemented in ICM (version 2.7, Molsoft LLC, San Diego, CA) (21Abagyan R. Totrov M. J. Mol. Biol. 1994; 235: 983-1002Crossref PubMed Scopus (803) Google Scholar). This method defines eight secondary structure classes from hydrogen bond patterns: α-helix (H), 310-helix (G), π-helix (I), extended strand (E), isolated β bridge (B), turn (T), bend (S), and coil (_). Here three classes of secondary structures were used as follows: helix (H, G, and I), strand (E), and loop (B, T, S, and _), since these three classes are employed by the method used for secondary structure prediction. Secondary structures were predicted using PHD (Profile network from HeiDelberg) (22Rost B. Sander C. J. Mol. Biol. 1993; 232: 584-599Crossref PubMed Scopus (2639) Google Scholar), a system of neural networks with an overall accuracy of about 72% (23Rost B. Sander C. Proteins. 1994; 19: 55-77Crossref PubMed Scopus (1337) Google Scholar). In 1978, Chou and Fasman (24Chou P.Y. Fasman G.D. Adv. Enzymol. Relat. Areas Mol. Biol. 1978; 47: 45-148PubMed Google Scholar) calculated the amino acid distributions in helices, Pα, and β-strands, Pβ, based on a set of 29 proteins. The P values are defined as the frequency of each amino acid residue in α-helices (or β-strands) divided by the average frequency of all residues in α-helices (or β-strands). We recalculated these values using stretches of at least five consecutive residues of helix (H) or β-strand (E) in the Protein Data Bank May data set described above. For this purpose transmembrane proteins were removed, resulting in a set of 1091 proteins. The resulting Pα and Pβ values are given in Table I.Table IPropensity values for α-helices (Pα) and β-strands (Pβ)Amino acidPαPβA1.46 (1.42)0.78 (0.83)C0.75 (0.70)1.26 (1.19)D0.83 (1.01)0.51 (0.54)E1.37 (1.51)0.69 (0.37)F0.97 (1.13)1.49 (1.38)G0.43 (0.57)0.69 values were calculated according to P.Y. Fasman G.D. Adv. Enzymol. Relat. Areas Mol. Biol. 1978; 47: 45-148PubMed Google from a set of 1091 proteins, for For each amino acid the Pα and Pβ values calculated from 1091 proteins are given without the values derived from a set of 29 proteins are given in P values that between the data are in in a new The values were calculated according to P.Y. Fasman G.D. Adv. Enzymol. Relat. Areas Mol. Biol. 1978; 47: 45-148PubMed Google from a set of 1091 proteins, for For each amino acid the Pα and Pβ values calculated from 1091 proteins are given without the values derived from a set of 29 proteins are given in P values that between the data are in SP-C was from (12Johansson J. Szyperski T. Curstedt T. Wüthrich K. Biochemistry. 1994; 33: 6015-6023Crossref PubMed Scopus (176) Google Scholar) and the → SP-C analogue was as described G. Gustafsson M. Vandenbussche G. Veldhuizen E. Griffiths W.J. Sjövall J. Haagsman H.P. Ruysschaert J.-M. Robertson B. Curstedt T. Johansson J. Eur. J. Biochem. 1998; 255: 116-124Crossref PubMed Scopus (84) Google transpeptidase fromStreptomyces R61 was a from and of and triacylglycerol lipase antarctica and human coagulation factor XIII were from For studies the three proteins were in pH at of SP-C and were at or in a in which SP-C a structure very similar to that in J. Szyperski T. Wüthrich K. FEBS Lett. 1995; PubMed Scopus Google Scholar). The protein were at 37 for the were at for SP-C and in the at different were determined by amino acid of For of the were in a of by for of were on by a was and the were with in The were and in a at A nonredundant set of protein sequences with known three-dimensional structures proteins, of amino acid was to PHD for secondary structure prediction. 37 of these proteins a or longer α-helix predicted on a from to to be in β-strand This be to as Secondary structure based on α-helix and β-strand values in with the PHD The of discordant stretches for segments and only proteins with discordant segments were amino acid sequences as well as determined and predicted secondary structures for the proteins with discordant The discordant segment of Aβ is also in the discordant segments of human and R. A. T. R. C. M. L. G. Wüthrich K. Proc. Natl. Acad. Sci. U. S. A. 2000; PubMed Scopus Google R. S. G. M. Glockshuber R. Wüthrich K. Nature. 1996; PubMed Scopus Google Scholar) are in addition to the discordant segment of H. S. H. K. Groth D. Mehlhorn I. Prusiner S.B. Cohen F.E. Proc. Natl. Acad. Sci. U. S. A. 1997; PubMed Scopus Google Scholar) found by the The proteins that contain segments a of structures from helical peptides to proteins with α/β and proteins, as well as and of from to The set three known the prion protein or discordant on to helix Aβ and SP-C and in the structures of the discordant segments be a for amyloid-forming proteins FEBS Lett. 1998; PubMed Scopus Google Scholar) a of and residues found in peptides by a W. J. J.D. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: PubMed Scopus Google Scholar) be of long discordant protein acid with determined and predicted secondary structure elements for all discordant and of and human The proteins are the of their discordant The proteins for which amyloid formation has been are by or in addition to the Protein Data Bank given for all The of each the experimentally determined helical segments as in which the amino acid sequences are The of the helices in the Protein Data Bank entries and in the proteins are In the where only is the Protein Data Bank entries to the In the the of the β-strands predicted by PHD are by where the for each residue is The for segments and residue in each are given in In these structures β-strands) predicted with high and and structures in an the proteins with discordant five are proteins or and The for α-helix formation in a from in C.M. Struct. Biol. 1994; 1: PubMed Scopus Google Scholar), and the secondary structure used are based mainly on proteins. which is derived from a and of its precursor and which is a transmembrane form amyloid in The proteins found a of and are with in the data or other proteins and In several the discordant helices harbor or For the and and harbor or residues in their helix W. R. R. W. Nature. 1992; PubMed Scopus Google Scholar, V. Protein Sci. 1998; 7: PubMed Scopus Google Scholar, Chem. Biol. 1995; Full Text PDF Scopus Google the helix of protein A contains several residues for R. A. M. C. M. Struct. Biol. 1999; 6: PubMed Scopus Google in the factor the discordant segment is in J. J. M. G. S. S. B. Nature. 1998; PubMed Scopus Google the helix of the bacteriorhodopsin the Eur. J. Biochem. 1992; PubMed Scopus Google and the of R61 transpeptidase is in the discordant helix H. B. J. Biol. Chem. Full Text PDF PubMed Google Scholar). R. S. M. R. G. K. FEBS Lett. 1998; PubMed Scopus Google Scholar) that to and that is a is in the part of helix 2, found to be discordant of the proteins long discordant helices, transpeptidase from triacylglycerol lipase from C. and human coagulation factor with and discordant segments were to for three proteins were found to form amyloid fibrils in at pH Thus, proteins with segments and with segments of residues have been and all form amyloid fibrils. The correlation between α/β discordance and fibril formation that may be a and with of the discordant proteins of all valine residues in the discordant segment of SP-C with a with helical as by and G. Gustafsson M. Vandenbussche G. Veldhuizen E. Griffiths W.J. Sjövall J. Haagsman H.P. Ruysschaert J.-M. Robertson B. Curstedt T. Johansson J. Eur. J. Biochem. 1998; 255: 116-124Crossref PubMed Scopus (84) Google Scholar). is in to the discordant native SP-C predicted to form an α-helical structure, and the of SP-C and striking differences SP-C to during the of incubation and but no of during the forms no fibrils or only fibrils of incubation at not on the other forms abundant fibrils at a (14Gustafsson M. Thyberg J. Näslund J. Eliasson E. Johansson J. FEBS Lett. 1999; 464: 138-142Crossref PubMed Scopus (96) Google Scholar). a synthetic analogue of that residues 14–23 and thus is of the stretch does not form amyloid fibrils under conditions where readily forms fibrils (11Tjernberg L.O. Callaway D.J. Tjernberg A. Hahne S. Lilliehook C. Terenius L. Thyberg J. Nordstedt C. J. Biol. Chem. 1999; 274: 12619-12625Abstract Full Text Full Text PDF PubMed Scopus (330) Google Scholar). with at positions and does not form whereas forms fibrils that are similar to formed by L.O. Näslund J. Johansson J. Thyberg J. Terenius L. Nordstedt C. J. Biol. Chem. 1996; Full Text Full Text PDF PubMed Scopus Google Scholar). Intriguingly, these the discordance of a predicted helix between residues and of secondary structure of and with the experimentally determined structure of described for and We experimentally determined nonredundant protein structures from Protein Data Bank with secondary structures predicted for the proteins using PHD and a proteins were found to contain a α-helix that is predicted to form a These proteins include associated with spongiform Aβ in Alzheimer's and lung SP-C that forms amyloid in pulmonary alveolar proteinosis and contains a discordant helix (positions data not and does not form amyloid. human with point → or → are both and (9Booth D.R. Sunde M. Bellotti V. Robinson C.V. Hutchinson W.L. Fraser P.E. Hawkins P.N. Dobson C.M. Radford S.E. Blake C.C.F. Pepys M.B. Nature. 1997; 385: 787-793Crossref PubMed Scopus (972) Google Scholar). to be whether the discordant helix of to the of the The proteins known to be associated with amyloid diseases (1Kelly J.W. Curr. Opin. Struct. Biol. 1996; 6: 11-17Crossref PubMed Scopus (568) Google Scholar, J.D. Annu. Rev. Biochem. 1992; 61: 947-975Crossref PubMed Scopus (408) Google Scholar) are all β proteins or experimentally determined three-dimensional proteins found to be human coagulation factor and C. antarctica triacylglycerol were and found to form amyloid fibrils upon incubation in at pH We also show that fibril formation and peptide is by the stretch of SP-C to a helix composed of residues that helix formation Likewise, fibril formation is when the discordant stretch of the Aβ peptide is removed or nondiscordant by of three residues (11Tjernberg L.O. Callaway D.J. Tjernberg A. Hahne S. Lilliehook C. Terenius L. Thyberg J. Nordstedt C. J. Biol. Chem. 1999; 274: 12619-12625Abstract Full Text Full Text PDF PubMed Scopus (330) Google Scholar, L.O. Näslund J. Johansson J. Thyberg J. Terenius L. Nordstedt C. J. Biol. Chem. 1996; Full Text Full Text PDF PubMed Scopus Google Scholar) is that are a of that amyloid fibrils be and the data suggest that long stretches of discordance in proteins amyloid fibril formation. that proteins with discordant helices can form where the helix has The high β-strand of these indicate that they are less to into a helical than are for which helices are in form β-sheets protein to fibril formation. This has been for of the SP-C helix is not by (13Szyperski T. Vandenbussche G. Curstedt T. Ruysschaert J.-M. Wüthrich K. Johansson J. Protein Sci. 1998; 7: 2533-2540Crossref PubMed Scopus (69) Google Scholar) or W. J. E. and J. in but the peptide forms β-sheet aggregates and amyloid fibrils (13Szyperski T. Vandenbussche G. Curstedt T. Ruysschaert J.-M. Wüthrich K. Johansson J. Protein Sci. 1998; 7: 2533-2540Crossref PubMed Scopus (69) Google M. Thyberg J. Näslund J. Eliasson E. Johansson J. FEBS Lett. 1999; 464: 138-142Crossref PubMed Scopus (96) Google Scholar). Proteins that are not known to form fibrils in can form fibrils under in vitro conditions that like of pH and of J.I. Sunde M. Dobson C.M. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: PubMed Scopus Google Scholar, A. M. G. Dobson C.M. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: PubMed Scopus Google Scholar). these studies has been that amyloid formation is not on the amino acid but be a of The indicate that also under fibril formation is more common than the other SP-C polyvaline → polyleucine and mutations of fibril that at least in these the is L.O. Näslund J. Johansson J. Thyberg J. Terenius L. Nordstedt C. J. Biol. Chem. 1996; Full Text Full Text PDF PubMed Scopus Google Scholar). The in between SP-C and its polyleucine analogue as a of fibril formation. of the fibril formation of proteins, and where the discordant helices have been may more on that amyloid fibril formation under of is whereas helices and of were predicted to be helical both with PHD and not in a of secondary structure, were for the helix that of can Z. J.-M. Baldwin Fletterick R.J. Prusiner S.B. Cohen F.E. Proc. Natl. Acad. Sci. U. S. A. 1994; PubMed Scopus Google Scholar). In the discordant segment of helix 2, the is to helix a and the is The of these for the are not known at the for the conversion of to PrPSc have been found Baldwin L. Prusiner S.B. Biochemistry. 1993; PubMed Scopus Google Scholar). In protein involves R. 1996; Full Text Full Text PDF PubMed Scopus Google Scholar). can in that may be and prone to H. J. Mehlhorn I. Groth D. Baldwin Prusiner S.B. Cohen F.E. Biochemistry. 1997; PubMed Scopus Google Scholar). of eight point to associated with inherited forms of prion in the of helix resulted in at a than that at which the other were when in (10Liemann S. Glockshuber R. Biochemistry. 1999; 38: 3258-3267Crossref PubMed Scopus (295) Google Scholar). Likewise, human helix rise to whereas and were W. J. Biol. Chem. 1998; Full Text Full Text PDF PubMed Scopus (176) Google Scholar). Amyloid is to be associated and the during the of the diseases (1Kelly J.W. Curr. Opin. Struct. Biol. 1996; 6: 11-17Crossref PubMed Scopus (568) Google Scholar, C.M. Trends Biochem. Sci. 1999; 24: 329-332Abstract Full Text Full Text PDF PubMed Scopus (1692) Google Scholar, J. V. R. J.D. J. 2000; PubMed Scopus Google Scholar). This that of amyloid formation may the occurrence of have been to that can fibril formation by with in fibrils or by that to peptides D.J. Nature. 1999; PubMed Scopus Google Scholar). suggest that helices are in the for proteins and that of these segments in helical amyloid formation. an to as the segments and specific and their in the proteins Aβ and are We are to Wüthrich and Tjernberg for on this and to for the experimentally determined structures from the Protein Data Bank. cellular form of prion protein amyloid β-peptide prion protein scrapie form of prion protein lung surfactant protein C → analogue of SP-C network from