573
Views
24
CrossRef citations to date
0
Altmetric
Research Paper

Left handed β helix models for mammalian prion fibrils

, , &
Pages 81-90 | Received 29 Jul 2008, Accepted 23 Sep 2008, Published online: 01 Oct 2008

References

  • Prusiner SB. Prusiner SB. Introduction to Prion biology and diseases. Prion biology and disease 2004; Cold Spring Harbor, NY Cold Spring Harbor Press 1 - 88
  • Cox DL, Lashuel HA, Lee KY, Singh RRP. The materials science of protein aggregation. MRS Bull 2005; 30:452 - 457
  • Caughey B, Baron GS. Prions and their partners in crime. Nature 2006; 443:803 - 810
  • Lansbury PT, Lashuel HA. Reversibility of prion-induced neurodegeneration. Nature 2006; 443:774 - 779
  • Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Doeli H, Schubert D, Riek R. Proc Natl Acad Sci USA 2005; 102:17342 - 17347
  • Petkova AT, Yau WM, Tycko R. Experimental contraints on quatemary structure in Alzheimer's amyloid fibrils. Biochemistry 2005; 45:498 - 512
  • Wasmer C, Lange A, Van Melckebeke H, Siemer AB, Riek R, Meier BH. Amyloid Fibrils of the HET-s(218–289) Prion form a β Solenoid with a Triangular Hydrophobic Core. Science 2008; 319:1523 - 1526
  • Govaerts C, Wille H, Prusiner SB, Cohen FE. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Nat Acad Sci USA 2004; 101:8342 - 8347
  • Tattum MH, Cohen-Krausz S, Kalili-Shirazi A, Jackson GS, Orolova EV, Collinge J, Clarke AR, Saibil HR. Elongated oligomers assemble into mammalian PrP amyloid fibrils. J Mol Biol 2006; 357:75 - 985
  • Jenkins J, Pickersgill R. The architecture of parallel β-helices and related folds. Prog Biophys Mol Biol 2001; 77:111 - 175
  • Choi JH, Govaerts C, May BCH, Cohen FE. Analysis of the sequence and structural features of the left-handed β-helical fold. Proteins, Structure, Function and Bioinformatics http://www3.interscience.wiley.com/tools/citex?clienttype=1&subtype=1&mode=1&versio n=1&id=117955077&redirect=/cgi-bin/fulltext/117955077/HTMLSTART
  • Yang S, Levine H, Onuchic JN, Cox DL. Structure of infectious prions: Stabilization by domain swapping. FASEB J 2005; 19:1778 - 1782
  • DeMarco ML, Daggett V. From conversion to aggregation: Protofibril formation of the Prion protein. Proc Nat Acad Sci USA 2004; 101:2293 - 2298
  • DeMarco ML, Silveira J, Caughey B, Daggett V. Structural properties of Prion protein protofibrils and fibrils: An experimental assessment of atomic models. Biochem 2006; 45:15573 - 15582
  • Guo JT, Wetzel R, Ying X. Molecular modeling of the core of Abeta amyloid fibrils. Proteins 2004; 57:357 - 364
  • Kishimoto A, Hasegawa K, Suzuki H, Taguchi H, Namba K, Yoshida M. Beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers. Biochem Biophys Res Comm 2004; 315:739 - 745
  • Shewmaker F, Ross ED, Tycko R, Wickner RB. Amyloids of shuffled prion domains that form Prions have a parallel in-register beta-sheet structure. Biochem 2008; 47:4000 - 4007
  • Wetzel R. Ideas of order for amyloid fibril structure. Structure 2002; 10:1031 - 1036
  • Stork M, Giese A, Kretzschmar HA, Tavan P. Molecular dynamics simulations indicate a possible role of parallel beta-helices in seeded aggregation of poly-gln. Biophys J 2005; 88:2442 - 2451
  • Zoghbi HY, Orr HT. Glutamine repeats and neurodegeneration. Ann Rev Neurosci 2000; 23:217 - 247
  • Chen SM, Ferrone FA, Wetzel R. Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation. Proc Nat Acad Sci USA 2002; 99:11884 - 11889
  • Perutz M, Finch JT, Berriman J, Lesk A. Amyloid fibers are water-filled nanotubes. Proc Nat Acad Sci USA 2002; 99:5591 - 5595
  • Sikorski P, Atkins E. New Model for Crystalline Polyglutamine Assemblies and their connection with Amyloid Fibrils. Biomacromol 2005; 6:425 - 432
  • Zanuy D, Gunasekaran K, Lesk AM, Nussinov R. Computational Study of the Fibril Organization of Polyglutamine Repeats Reveals a Common Motif Identified in β-helices. J Mol Biol 2006; 358:330 - 345
  • Wang X, Vitalis A, Wyczlkowski MA, Pappu RV. Characterizing the Conformational Ensemble of Monomeric Polyglutamine. Proteins: Structure, Function and Bioinformatics 2006; 63:297 - 311
  • Sharma D, Shinchuk LM, Inouye H, Wetzel R, Kirscher DA. Polyglutamine Homopolymers having 8–45 residues Form Slablike β-Crystallite Assemblies. Proteins 2005; 61:398 - 411
  • See the EMD Database at http://www.ebi.ac.uk/msd-srv/emsearch/index.html
  • Safar J, Roller PP, Gajdusek DC, Gibbs CJ. Conformational transitions, dissociation and unfolding of scrapie amyloid (Prion) protein. J Biol Chem 1993; 268:20276 - 20284
  • Pan KM, Baldwin M, Nguyen J, Gasset M, Serban A, Groth D, Mehlhorn I, Huang ZW, Fletterick RJ, Cohen FE, Prusiner SB. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion protein. Proc Nat Acad Sci USA 1993; 90:10962 - 10966
  • Legname G, Baskakov IV, Nguyen H-oB, Riesner D, Cohen FE, DeArmond SJ, Prusiner SB. Synthetic mammalian Prions. Science 2004; 305:673 - 676
  • Zahn R, Liu A, Luhrs T, Riek R, von Schroetter C, Lopez-Garcia F, Billeter M, Calzolai L, Wider G, Wuthrich. NMR solution structure of the human prion protein. Proc Natl Acad Sci USA 2000; 97:145 - 150
  • Langedijk JPM, Fuentes G, Boshulzen R, Bonvin AMJJ. Two-rung model of a left-handed β-helix for Prions explains species barrier and strain variation in Transmissible Spongiform Encephalopathies. J Mol Biol 2006; 360:907 - 920
  • Bennett MJ, Sawaya MR, Eisenberg D. Deposition diseases and 3D domain swapping. Structure 2006; 14:811 - 824
  • Lewis PA, Tattum MH, Jones S, Bhelt D, Batchelor M, Clarke AR, Collinge J, Jackson GS. Codon 129 polymorphism of the human prion protein influences the kinetics of amyloid formation. J Gen Virol 2006; 87:2443 - 2449
  • Tahiri-Alaoui A, Gill AC, Disterer P, James W. Methionine 129 variant of human Prion protein oligomerizes more rapidly than the valine 129 variant. J Biol Chem 2004; 279:31390 - 31397
  • Dima RI, Thirumalai D. Perturbation of the secondary structure of the scrapie Prion protein under conditions that alter infectivity. Proc Nat Acad Sci USA 2004; 101:15335 - 15340
  • Lu X, Wintrode PL, Surewicz WK. Beta-sheet core of hman prion protein amyloid fibrils as determined by hydrogen-deuterium exchange. Proc Nat Acad Sci USA 2007; 104:1510 - 1515
  • Paramithiotis E, et al. A prion protein epitope selective for the pathologically misfolded conformation. Nature Med 2003; 9:893 - 899
  • Sawaya MR, et al. Atomic structures of amyloid cross-b spines reveal varied steric zippers. Nature 2007; 447:453 - 457
  • Cobb NJ, Sonnichsen FD, Mchaourab H, Surewicz WK. Molecular architecture of human prion protein amyloid: A parallel, in register β-structure. PNAS 2007; 104:18946 - 18951
  • Baskakov IV, Legname G, Prusiner SB, Cohen FE. Folding of prion protein to its native alpha-helical conformation is under kinetic control. J Biol Chem 2001; 23:19687 - 19690
  • Rezaei H, Choiset Y, Eghiaian F, Terguer E, Mentre P, Debehy P, Grosclaude J, Haertle T. Amyloidogenic Unfolding Intermediates Differentiate Sheep Prion Variants. J Mol Biol 2002; 322:799 - 814
  • Moroncini G, Kanu N, Lolforosi L, Abalos G, Telling GC, Head M, Ironside J, Brockes JP, Burton DR, Williamson RA. Motif-grafted antibodies containing the replicative interface of cellular PrP are specific for PrP. Proc Nat Acad Sci USA 2004; 101:10404 - 10409
  • Novitskaya V, Makarava N, Bellon A, Bocharova OV, Bronstein IB, Williamson RA, Baskakov IV. Probing the conformation of the Prion protein within a single amyloid fibril using a novel immunoconformational assay. J Biol Chem 2006; 281:15536 - 15545
  • Will RG, Alpers MP, Dormont D, Schonberger LB. Prusiner SB. Introduction to Prion biology and diseases. Prion biology and disease 2004; Cold Spring Harbor, NY Cold Spring Harbor Press 629 - 672
  • Govaerts C, Wille J, Prusiner SB, Cohen FE. Prusiner SB. Introduction to Prion biology and diseases. Prion biology and disease 2004; Cold Spring Harbor, NY Cold Spring Harbor Press 243 - 282
  • Wells GAH, Wilesmith JW. Prusiner SB. Introduction to Prion biology and diseases. Prion biology and disease 2004; Cold Spring Harbor, NY Cold Spring Harbor Press 595 - 628
  • Gregoret LM, Rader SD, Fletterick RJ, Cohen FE. Hydrogen bonds involving sulfur atoms in proteins. Proteins 1991; 9:99 - 107
  • McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994; 238:777 - 793
  • Allen FH, Bird CM, Rowland RS, Raithby PR. Hydrogen-Bond Acceptor and Donor Properties of Divalent Sulfur (Y-S-Z and R-S-H). Acta Cryst 1997; 53:696 - 701
  • Valdes-Martinez J, Hernandez-Ortega S, Rubio M, Li DT, Swearingen JK, Kaminsky W, Kelman DR, West DX. Study of the sulfur atom as hydrogen bond acceptor in N(2)-pyridylmethyl-N'-arylthioureas. J Chem Cryst 2004; 34:533 - 540
  • Rablen PR, Lockman JW, Jorgensen WL. Ab initio study of hydrogen-bonded complexes of small organic molecules with water. J Phys Chem A 1998; 102:3782 - 3797
  • Wennmohs F, Staemmler V, Schindler M. Theoretical investigation of weak hydrogen bonds to sulfur. J Chem Phys 2003; 119:3208 - 3218
  • Wennmohs F, Schindler M. Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high-level ab initio interaction energies. J Comp Chem 2005; 26:283 - 293
  • Lee HS, Brown P, Cervenakova L, Garruto RM, Alpers MP, Gajdusek DC, Goldfarb LG. Increased susceptibility to Kuru of carriers of the PRNP 129 methionine/methionine genotype. J Infect Dis 2001; 183:192 - 196
  • Telling GC, Scott M, Mastrianni J, Gabizon R, Torchia M, Cohen FE, DeArmond SJ, Prusiner SB. Prion propagation in mice expressing human and chimeric PrP transgenes implicates the interaction of cellular PrP with another protein. Cell 1995; 83:79 - 90
  • Brandel JP. Distribution of codon 129 genotype in human growth hormone-treated CJD patients in France and the UK. Lancet 2003; 362:128 - 130
  • Wadsworth JDF. Human Prion protein with valine 129 prevents expression of variant CJD phenotype. Science 2004; 306:1793 - 1796
  • Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000; 40:389 - 408
  • Luehrs T, Zahn R, Wuetrich K. Amyloid formation by recombinant full-length Prion proteins in phospholipid bicelle solutions. J Mol Biol 2006; 57:833 - 841
  • Slepoy A, Singh RRP, Pazmandi F, Kulkarni RV, Cox DL. Statistical mechanics of prion diseases. Phys Rev Lett 2001; 87:058101
  • Kulkarni RV, Slepoy A, Singh RRP, Cox DL, Pazmandi F. Simulations of oligomeric ontermediates in prion diseases. Biophys J 2003; 85:2213 - 2223
  • Prisner T, Rohrer M, MacMillan F. PULSED EPR SPECTROSCOPY: Biological application. Ann Rev Phys Chem 2001; 52:279 - 313
  • Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ. The amber biomolecular simulation programs. J Comput Chem 2005; 26:1668 - 1688
  • Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem 2004; 25:1605 - 1612
  • Guex N, Peitsch MC. Swiss-Model and the Swiss-PDBViewer: an environment for It
  • Humphrey W, Dalke A, Schulten K. Visual Molecular Dynamics. J Mol Graph 1996; 14:33 - 38
  • Kehoe LE, Snidwongse J, Courvalin P, Rafferty JB, Murray IA. Structural basis of synercid (Quinupristin-Dalfopristin) resistance in gram-positive bacterial pathogens. J Biol Chem 2003; 278:29963 - 29970
  • Beaman TW, Vogel KW, Drueckhammer DG, Blanchard JS, Roderick SL. Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase. Protein Sci 2002; 11:974 - 979
  • Olsen LR, Huang B, Vetting MW, Roderick SL. Structure of serine acetyltransferase in complexes with CoA and its cysteine feedback inhibitor. Biochemistry 2004; 43:6013 - 6019
  • Pye VE, Tingey AP, Robson RL, Moody PC. The structure and mechanism of serine acetyltransferase from Escherichia coli. J Biol Chem 2004; 279:40729 - 40736
  • Kostrewa D, D'Arcy A, Takacs B, Kamber M. Crystal structures of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase, GlmU, in apo form at 2.33 A resolution and in complex with UDP-N-acetylglucosamine and Mg(2+) at 1.96 A resolution. J Mol Biol 2001; 305:279 - 289
  • Raetz CR, Roderick SL. A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 1995; 270:997 - 1000