Evidence for assembly of prions with left-handed β-helices into trimers

Studies using low-resolution fiber diffraction, electron microscopy, and atomic force microscopy on various amyloid fibrils indicate that the misfolded conformers must be modular, compact, and adopt a cross-β structure. In an earlier study, we used electron crystallography to delineate molecular models of the N-terminally truncated, disease-causing isoform (PrPSc) of the prion protein, designated PrP 27–30, which polymerizes into amyloid fibrils, but we were unable to choose between a trimeric or hexameric arrangement of right- or left-handed β-helical models. From a study of 119 all-β folds observed in globular proteins, we have now determined that, if PrPSc follows a known protein fold, it adopts either a β-sandwich or parallel β-helical architecture. With increasing evidence arguing for a parallel β-sheet organization in amyloids, we contend that the sequence of PrP is compatible with a parallel left-handed β-helical fold. Left-handed β-helices readily form trimers, providing a natural template for a trimeric model of PrPSc. This trimeric model accommodates the PrP sequence from residues 89–175 in a β-helical conformation with the C terminus (residues 176–227), retaining the disulfide-linked α-helical conformation observed in the normal cellular isoform. In addition, the proposed model matches the structural constraints of the PrP 27–30 crystals, positioning residues 141–176 and the N-linked sugars appropriately. Our parallel left-handed β-helical model provides a coherent framework that is consistent with many structural, biochemical, immunological, and propagation features of prions. Moreover, the parallel left-handed β-helical model for PrPSc may provide important clues to the structure of filaments found in some other neurodegenerative diseases.

[1]  F. Cohen,et al.  Separation of scrapie prion infectivity from PrP amyloid polymers. , 1996, Journal of molecular biology.

[2]  J. Kelly,et al.  The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. , 1998, Current opinion in structural biology.

[3]  K Wüthrich,et al.  NMR structures of three single-residue variants of the human prion protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[4]  M. Braunfeld,et al.  Identification of prion amyloid filaments in scrapie-infected brain , 1985, Cell.

[5]  Adrian A Canutescu,et al.  A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.

[6]  A. Aguzzi,et al.  Soluble Dimeric Prion Protein Binds PrPSc In Vivo and Antagonizes Prion Disease , 2003, Cell.

[7]  Ralf Langen,et al.  Structural Organization of α-Synuclein Fibrils Studied by Site-directed Spin Labeling* , 2003, Journal of Biological Chemistry.

[8]  S. Prusiner,et al.  Scrapie prion rod formation in vitro requires both detergent extraction and limited proteolysis , 1991, Journal of virology.

[9]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[10]  S. Prusiner,et al.  Shattuck lecture--neurodegenerative diseases and prions. , 2001, The New England journal of medicine.

[11]  Roland L. Dunbrack,et al.  Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. , 1997, Journal of molecular biology.

[12]  S. Prusiner,et al.  Ablation of the prion protein (PrP) gene in mice prevents scrapie and facilitates production of anti-PrP antibodies. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  S. Prusiner,et al.  Scrapie prions aggregate to form amyloid-like birefringent rods , 1983, Cell.

[14]  Elena Orlova,et al.  Cryo‐electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing , 1999, The EMBO journal.

[15]  Christopher M Dobson,et al.  The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation , 2002, The EMBO journal.

[16]  T. Creighton.  Proteins: Structures and Molecular Properties , 1986 .

[17]  遠藤 肇,et al.  :"Tohoku J. Exp. Med." による , 1964 .

[18]  F E Cohen,et al.  A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. , 1997, Journal of molecular biology.

[19]  D. Eisenberg.  Proteins. Structures and molecular properties, T.E. Creighton. W. H. Freeman and Company, New York (1984), 515, $36.95 , 1985 .

[20]  M. Hoshino,et al.  Mapping the core of the β2-microglobulin amyloid fibril by H/D exchange , 2002, Nature Structural Biology.

[21]  F. Cohen,et al.  Prion Protein Biology , 1998, Cell.

[22]  Pascale Cossart,et al.  Sequence Profile of the Parallel β Helix in the Pectate Lyase Superfamily , 1998 .

[23]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[24]  P E Wright,et al.  Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. , 1993, Science.

[25]  Z. Jia,et al.  Crystal structure of beta-helical antifreeze protein points to a general ice binding model. , 2002, Structure.

[26]  F. Cohen,et al.  Pathway Complexity of Prion Protein Assembly into Amyloid* , 2002, The Journal of Biological Chemistry.

[27]  Patrice Koehl,et al.  The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..

[28]  R. Riek,et al.  NMR structure of the mouse prion protein domain PrP(121–231) , 1996, Nature.

[29]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[30]  P. Lansbury,et al.  Amyloid fibrillogenesis: themes and variations. , 2000, Current opinion in structural biology.

[31]  J. Richardson,et al.  Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[32]  C. Blake,et al.  From the globular to the fibrous state: protein structure and structural conversion in amyloid formation , 1998, Quarterly Reviews of Biophysics.

[33]  R. Pickersgill,et al.  The architecture of parallel β-helices and related folds , 2001 .

[34]  F. Cohen,et al.  Prion Protein of 106 Residues Creates an Artificial Transmission Barrier for Prion Replication in Transgenic Mice , 1999, Cell.

[35]  R. Wetzel.  Ideas of order for amyloid fibril structure. , 2002, Structure.

[36]  J. Miller,et al.  Radiation target analysis of glycoproteins. , 1986, Analytical biochemistry.

[37]  William R. Taylor,et al.  Analysis and prediction of protein β-sheet structures by a combinatorial approach , 1980, Nature.

[38]  L. Regan,et al.  A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy. , 2003, Biophysical journal.

[39]  Fred E. Cohen,et al.  Folding of Prion Protein to Its Native α-Helical Conformation Is under Kinetic Control* , 2001, The Journal of Biological Chemistry.

[40]  L. Hood,et al.  Purification and properties of the cellular and scrapie hamster prion proteins. , 1988, European journal of biochemistry.

[41]  Christopher M. Dobson,et al.  The protofilament structure of insulin amyloid fibrils , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[42]  H. Diringer,et al.  Absence of autoantibodies against neurofilament proteins in the sera of scrapie infected mice. , 1985, The Tohoku journal of experimental medicine.

[43]  R. Seckler,et al.  Formation of Fibrous Aggregates from a Non-native Intermediate: The Isolated P22 Tailspike β-Helix Domain* , 1999, The Journal of Biological Chemistry.

[44]  L. Serpell,et al.  Common core structure of amyloid fibrils by synchrotron X-ray diffraction. , 1997, Journal of molecular biology.

[45]  F. Cohen,et al.  Recombinant scrapie-like prion protein of 106 amino acids is soluble. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[46]  J T Finch,et al.  Amyloid fibers are water-filled nanotubes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[47]  S. Prusiner,et al.  Scrapie prion liposomes and rods exhibit target sizes of 55,000 Da. , 1988, Virology.

[48]  V. Georgiev.  Virology , 1955, Nature.

[49]  Manish S. Shah,et al.  A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes , 1993, Cell.

[50]  F. Cohen,et al.  Dominant-negative inhibition of prion replication in transgenic mice , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[51]  R. Glockshuber,et al.  Extremely rapid folding of the C-terminal domain of the prion protein without kinetic intermediates , 1999, Nature Structural Biology.

[52]  C. Dobson.  The structural basis of protein folding and its links with human disease. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[53]  R. Seckler,et al.  P22 tailspike folding mutants revisited: effects on the thermodynamic stability of the isolated beta-helix domain. , 1998, Journal of molecular biology.

[54]  Ying Xu,et al.  Mapping abeta amyloid fibril secondary structure using scanning proline mutagenesis. , 2004, Journal of molecular biology.

[55]  R. Leapman,et al.  A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[57]  M. Vincent,et al.  AB INITIO QUANTUM CHEMICAL CALCULATIONS ON URANYL UO22+, PLUTONYL PUO22+, AND THEIR NITRATES AND SULFATES , 1995 .

[58]  David A Agard,et al.  Structural studies of the scrapie prion protein by electron crystallography , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[59]  M. DePristo,et al.  Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles , 2003, Proteins.