See How They Grow: Structure of Amyloid-β Fibrils

Current interest in the toxic mechanisms of oligomeric amyloid-β proteins notwithstanding, the larger fibrils this protein forms also are neurotoxic in their own right. Recent structural studies on prions and other amyloid-forming proteins have laid out the basic architectural underpinnings of the initiation and propagation of toxic fibrils (see ARF related news story). But for the Alzheimer amyloid, the devil truly is in the details, and gaining a molecular-level understanding of how the Aβ1-42 peptide stacks up is needed to answer some pressing questions: How exactly do fibrils form? How can they be stopped? How are they toxic to neurons?

To get at these questions, researchers in the lab of Roland Riek and collaborators at the Salk Institute in San Diego and in Lausanne and Basel, Switzerland, combined their own NMR, mutagenesis, and cryoelectron microscopy studies with existing data to determine the 3D structure of the Aβ1-42 fibril. Their results, published this week in PNAS online, show how peptide sequence and conformation drive Aβ1-42 fibril growth, and explain how one fibrillization inhibitor may stop it.

All amyloids form a cross-β structure, in which two parallel β sheets run along the fiber axis. Using NMR, first author Thorsten Lührs and colleagues showed that the two β sheets in the Alzheimer amyloid form from β1 and β2 strands spanning amino acids 18-26 and 31-42, respectively. Joined by a turn, the two strands form a U shape, and multiple peptides stack to form the fiber, held together by hydrogen bonds between in-register aligned β strands. By modeling and mutagenesis, the researchers determined that between the two β sheets there are three specific side-chain interactions. One is a salt bridge between the β1 strand and the linking region, and the other two are hydrophobic interactions between residues in the β1 and β2 strands.

A set of experiments that followed fiber formation using a variety of mutated Aβ1-42 peptides suggested that the contacts between β strands spanned two adjacent peptides. In particular, the modeling suggests that the D23 residue of a β1 strand reaches down to make a salt bridge with the K28 of the hinge region of the peptide underneath it in the stack. The two side-chain-specific hydrophobic interactions occur between the β1 strand of one peptide and the β2 strand of the peptide below it, relative to the direction of fibril growth. From this, the authors concluded that the Aβ1-42 fibrils are stabilized by intermolecular domain swapping interactions similar to those seen in other amyloids (see ARF related news story).

The directional intermolecular contact pattern exposes a hydrophobic groove on the growing end of the fiber where new Aβ1-42 monomers could bind. This groove also makes a welcome landing site for peptide analogs of residues 17-21 that have been shown to inhibit fiber growth (Gordon et al., 2001). The identification of this site may aid the design of additional inhibitors, the authors write.

The Aβ mutants used in these studies were observed to form a variety of structures, and the authors decided to test whether they could see a structure-toxicity relationship using a cultured neuronal cell line. Despite having long or short fibrils, or seed-like morphologies, all of the variants displayed neurotoxicity at approximately similar concentrations as did a wild-type control peptide (Aβ25-35). The most toxic mixtures contained fibrils, but enhanced toxicity was also seen with some oligomers, providing further evidence that harmful amyloid comes in several guises.—Pat McCaffrey

Comments

    • User Profile Image David Teplow
      David Geffen School of Medicine at UCLA
    • Posted:

    The work by Luhrs et al. truly is a tour de force that integrates hydrogen exchange/NMR studies, electron microscopy, thioflavin T-binding, MTT assays, and molecular modeling into studies of the structure of fibrils formed by wild-type Aβ42 and a variety of rationally designed mutants. The result is a provocative model of the organization of Aβ protofilaments, the component structures comprising the mature 10 nm amyloid-type fibrils.

    Evaluation of the work requires answers to two questions: Is the model correct, and is the model relevant? Additional experimentation will be required to provide these answers.

    The clever single (asymmetric) and multiple (symmetric) amino acid substitution experiments performed by Luhrs et al. yield data consistent with their initial postulation of two β-strand regions connected by a short turn. The molecular modeling studies produce a model with low root-mean-square deviation (RMSD) error, again suggesting consistency and correctness of the derived protofilament structure. However, as with any modeling endeavor, the results depend on the assumptions. For example, the Luhrs model assumes the correctness of a certain feature of an earlier model, that of Robert Tycko's group, and thus becomes a "model based on a model based on experimental data" (with apologies to Professor Dan Kirschner for stealing his line).
    The Luhrs model also integrates experimental data suggesting Met35 is not involved in intersheet side-chain packing. However, substantial experimental data exist showing that Met35 oxidation interferes significantly with Aβ aggregation (e.g., see Hou et al., 2002; Hou et al., 2004; Butterfield and Boyd-Kimball, 2005; Palmblad et al., 2002; Bitan et al., 2003).

    These studies emphasize an important structural role for Met35 in fibril formation, one that can be rationalized mechanistically by models such as that of the Tycko group and those derived by molecular dynamics simulations (Urbanc et al., 2004). The contribution of Met35 to fibril formation is consistent with the fact that fibril formation of the [35L]Aβ(1-42) peptides used in the study of Luhrs et al. occurred over a relatively long time period (two months).

    The use of oxidized Aβ (Met35 sulfoxide) also raises the question of relevance. What is the primary structure of the Aβ peptide(s) in vivo that gives rise to fibrils? Are the fibrils thus formed structurally equivalent to those studied by Luhrs et al? Evidence suggests that the predominant Aβ species is not oxidized. In addition, a large and increasing body of work supports the hypothesis that the most potent neurotoxins in Alzheimer disease and other diseases (e.g., prion diseases, see Silveira et al., 2005) may be oligomers and not fibrils. It would be exciting and informative if the approach of Luhrs et al. were applied to an analysis of the structure and dynamics of oligomer formation.

    In conclusion, the fine work of Luhrs et al. provides a wonderful working model of Aβ protofilament structure that is rich in testable hypotheses.

    References:

    Hou L, Kang I, Marchant RE, Zagorski MG. Methionine 35 oxidation reduces fibril assembly of the amyloid abeta-(1-42) peptide of Alzheimer's disease. J Biol Chem. 2002 Oct 25;277(43):40173-6. PubMed.

    Hou L, Shao H, Zhang Y, Li H, Menon NK, Neuhaus EB, Brewer JM, Byeon IJ, Ray DG, Vitek MP, Iwashita T, Makula RA, Przybyla AB, Zagorski MG. Solution NMR studies of the A beta(1-40) and A beta(1-42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation. J Am Chem Soc. 2004 Feb 25;126(7):1992-2005. PubMed.

    Butterfield DA, Boyd-Kimball D. The critical role of methionine 35 in Alzheimer's amyloid beta-peptide (1-42)-induced oxidative stress and neurotoxicity. Biochim Biophys Acta. 2005 Jan 17;1703(2):149-56. PubMed.

    Palmblad M, Westlind-Danielsson A, Bergquist J. Oxidation of methionine 35 attenuates formation of amyloid beta -peptide 1-40 oligomers. J Biol Chem. 2002 May 31;277(22):19506-10. PubMed.

    Bitan G, Tarus B, Vollers SS, Lashuel HA, Condron MM, Straub JE, Teplow DB. A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization. J Am Chem Soc. 2003 Dec 17;125(50):15359-65. PubMed.

    Urbanc B, Cruz L, Yun S, Buldyrev SV, Bitan G, Teplow DB, Stanley HE. In silico study of amyloid beta-protein folding and oligomerization. Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17345-50. PubMed.

    Silveira JR, Raymond GJ, Hughson AG, Race RE, Sim VL, Hayes SF, Caughey B. The most infectious prion protein particles. Nature. 2005 Sep 8;437(7056):257-61. PubMed.

    View all comments by David Teplow

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References

News Citations

  1. Making Heads and Tails of Prion Amyloid
  2. Size, Shape, Swapping—What Makes a Toxic Fiber?

Paper Citations

  1. Gordon DJ, Sciarretta KL, Meredith SC. Inhibition of beta-amyloid(40) fibrillogenesis and disassembly of beta-amyloid(40) fibrils by short beta-amyloid congeners containing N-methyl amino acids at alternate residues. Biochemistry. 2001 Jul 27;40(28):8237-45. PubMed.

Further Reading

Papers

  1. Bieler S, Soto C. Beta-sheet breakers for Alzheimer's disease therapy. Curr Drug Targets. 2004 Aug;5(6):553-8. PubMed.

Primary Papers

  1. Lührs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Döbeli H, Schubert D, Riek R. 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17342-7. PubMed.

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