Models Of Amyloid Fibrils Research Articles

Towards modeling of amyloid fibril structures

Amyloid fibrils are associated with a number of debilitating diseases, including Alzheimer's disease and variant Creutzfeldt-Jakob disease. The elucidation of the structure of amyloid fibrils is an important step toward understanding the mechanism of amyloid formation and developing therapeutic agents for amyloid diseases. Despite great interests and substantial efforts from various research communities, deriving high-resolution structures of amyloid fibrils remains a challenging problem, due to the insolubility and non-crystalline nature of the fibrils. An array of experimental methods, such as electron microscopy, fiber diffraction, hydrogen-deuterium exchange, solid-state NMR, electron paramagnetic resonance spectroscopy and biochemical approaches, have been explored to study the problem, having yielded considerable amount of, though still partial, information about the fibril conformation. Computational modeling techniques can be used to predict and build structural models of amyloid fibrils, utilizing the available experimental data. Here, we describe a few computational methods for modeling of aggregate and fibril structures with a focus on protein threading-based approaches and discuss the challenging issues ahead.

Binding mode of Thioflavin T in insulin amyloid fibrils

Amyloid fibrils share various common structural features and their presence can be detected by Thioflavin T (ThT). In this paper, the binding mode of ThT to insulin amyloid fibrils was examined. Scatchard analysis and isothermal titration calorimetry (ITC) showed at least two binding site populations. The binding site population with the strongest binding was responsible for the characteristic ThT fluorescence. This binding had a capacity of about 0.1 moles of ThT bound per mole of insulin in fibril form. The binding capacity was unaffected by pH, but the affinity was lowest at low pH. Notably, presence of a third binding process prior to the other processes was suggested by ITC. Binding of ThT resulted in only minor changes in the fibril structure according to the X-ray diffraction patterns, where a slightly more dominant equatorial reflection at 16 Å relative to the intersheet distance of 11 Å was observed. No change in the interstrand distance of 4.8 Å was observed. On the basis of our results, we propose that ThT binds in cavities running parallel to the fibril axis, e.g., between the protofilaments forming the fibrils. Such cavities have been proposed previously in insulin fibrils and several other amyloid fibril models.

Study on the binding of Thioflavin T to β-sheet-rich and non-β-sheet cavities

Amyloid fibril formation plays a role in more than 20 diseases including Alzheimer’s disease. In vitro detection of these fibrils is often performed using Thioflavin T (ThT), though the ThT binding mode is largely unknown. In the present study, spectral properties of ThT in binding environments representing β-sheet-rich and non-β-sheet cavities were examined. Acetylcholinesterase and γ-cyclodextrin induced a characteristic ThT fluorescence similar to that with amyloid fibrils, whereas β-cyclodextrin and the β-sheet-rich transthyretin did not. The cavities of acetylcholinesterase and γ-cyclodextrin were of similar diameter and only these cavities could accommodate two ThT ions according to molecular modelling. Binding stoichiometry studies also showed a possible binding of two ThT ions. Thus, the characteristic ThT fluorescence is induced in cavities with a diameter of 8–9 Å and a length able to accommodate the entire length of the ThT ion. The importance of a cavity diameter capable of binding two ThT ions, among others, indicates that an excimer formation is a plausible mechanism for the characteristic fluorescence. We propose a similar ThT binding mode in amyloid fibrils, where cavities of an appropriate size running parallel to the fibril axis have previously been proposed in several amyloid fibril models.

Structural Model of the Amyloid Fibril Formed by β2-Microglobulin #21−31 Fragment Based on Vibrational Spectroscopy

A structural model of amyloid fibril formed by the #21-31 fragment of beta2-microglobulin is proposed from microscope IR measurements on specifically 13C-labeled peptide fibrils and Raman spectra of the dispersed fibril solution. The 13C-shifted amide frequency indicated the secondary structure of the labeled residues. The IR spectra have demonstrated that the region between F22 and V27 forms the core part with the extended beta-sheet structure. Raman spectra indicated the formation of a dimer with a disulfide bridge between C25 residues.

The Parallel Superpleated Beta-structure as a Model for Amyloid Fibrils of Human Amylin

Human amylin is a 37 amino acid residue peptide hormone whose fibrillogenesis has been correlated with type 2 diabetes. These fibrils are rope-like bundles of several 5nm diameter protofilaments. Here, we propose, as a model for the protofilament, a variant of the parallel superpleated beta-structure previously derived for amyloid filaments of the yeast prion Ure2p. In the amylin model, individual polypeptides from residues 9 to 37 have a planar S-shaped fold with three beta-strands. These serpentines are stacked in register, with a 0.47 nm axial rise and a small rotational twist per step, generating an array of three parallel beta-sheets in cross-beta conformation. The interior, the two "bays" sandwiched between adjacent sheets, are occupied by non-polar and by polar/uncharged residues that are predicted to form H-bonded ladders, similar to those found in beta-helical proteins. The N-terminal peptide containing a disulfide bond occupies an extraneous peripheral position in the protofilament. The left-handed twist of the beta-sheets is shown to underlie left-handed coiling of amylin protofilaments in fibrils. The model is consistent with current biophysical, biochemical and genetic data and, in particular, affords a plausible explanation for why rodent amylin does not form fibrils.

A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR.

We present a structural model for amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)), based on a set of experimental constraints from solid state NMR spectroscopy. The model additionally incorporates the cross-beta structural motif established by x-ray fiber diffraction and satisfies constraints on Abeta(1-40) fibril dimensions and mass-per-length determined from electron microscopy. Approximately the first 10 residues of Abeta(1-40) are structurally disordered in the fibrils. Residues 12-24 and 30-40 adopt beta-strand conformations and form parallel beta-sheets through intermolecular hydrogen bonding. Residues 25-29 contain a bend of the peptide backbone that brings the two beta-sheets in contact through sidechain-sidechain interactions. A single cross-beta unit is then a double-layered beta-sheet structure with a hydrophobic core and one hydrophobic face. The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-beta units with their hydrophobic faces juxtaposed.

Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks.

Amyloid and prion diseases appear to stem from the conversion of normally folded proteins into insoluble, fiber-like assemblies. Despite numerous structural studies, a detailed molecular characterization of amyloid fibrils remains elusive. In particular, models of amyloid fibrils proposed thus far have not adequately defined the constituent protein subunit interactions. To further our understanding of amyloid structure, we employed thiol-specific cross-linking and site-directed spin labeling to identify specific protein-protein associations in transthyretin (TTR) amyloid fibrils. We find that certain cysteine mutants of TTR, when dimerized by chemical cross-linkers, still form fibers under typical in vitro fibrillogenic conditions. In addition, site-directed spin labeling of many residues at the natural dimer interface reveals that their spatial proximity is preserved in the fibrillar state even in the absence of cross-linking constraints. Here, we present the first view of a subunit interface in TTR fibers and show that it is very similar to one of the natural dimeric interchain associations evident in the structure of soluble TTR. The results clarify varied models of amyloidogenesis by demonstrating that transthyretin amyloid fibrils may assemble from oligomeric protein building blocks rather than structurally rearranged monomers.

Amyloids protect the silkmoth oocyte and embryo

Chorion is the major component of silkmoth eggshell. More than 95% of its dry mass consists of proteins that have remarkable mechanical and chemical properties protecting the oocyte and the developing embryo from a wide range of environmental hazards. We present data from electron microscopy (negative staining and shadowing), X-ray diffraction and modeling studies of synthetic peptide analogues of silkmoth chorion proteins indicating that chorion is a natural amyloid. The folding and self-assembly models of chorion peptides strongly support the β-sheet helix model of amyloid fibrils proposed recently by Blake and Serpell [Structure 4 (1996) 989–998].

Study of α-helix to β-strand to β-sheet transitions in amyloid: the role of segregated hydrophobic β-strands

A conformational analysis including three polypeptide chains known to be amyloidogenic and neurotoxic has shown the occurrence of low probability hydrophobic β-strands stabilized by intramolecular interactions. It is argued that by engaging in non-bonded and hydrophobic interactions these β-strands seed the assembly of β-sheets in amyloid fibrils following a non-cooperative mechanism dissimilar to β-sheet folding in proteins. Molecular models of amyloid fibrils formed by such β-strand templates were built. It is shown that the parallel alignment of β-strands creates an extensive hydrophobic surface whereas the antiparallel alignment causes the formation of hydrophobic and hydrophilic aggregates. A comparison with experimental data and previous calculations is established.