Direct Observation of Nucleation and Growth in Amyloid Self-Assembly

Direct Observation of Nucleation and Growth in Amyloid Self-Assembl

Direct Observation of Nucleation and Growth in Amyloid Self-Assembly

Direct Observation of Nucleation and Growth in Amyloid Self-Assembl

Direct Observation of Nucleation and Growth in Amyloid Self-Assembly

Direct Observation of Nucleation and Growth in Amyloid Self-Assembl

Modulating Amyloid Self-Assembly and Fibril Morphology with Zn(II)

Metal ions (Zn(II)) are demonstrated as probes of amyloid structure in simple segments of the Aβ peptide, Aβ(13−21). By restricting the possible metal binding sites to His13/His14 dyad, we show that Zn2+ can specifically control the rate of self-assembly and dramatically regulate amyloid morphology via distinct coordination environments as characterized by X-ray absorption spectroscopy. The data establish that the single His13 is sufficient to coordinate Zn2+ productively for typical amyloid fiber formation, while a distinct Zn2+ coordination environment can be accessed in the presence of His13/Hi14 dyad to stabilize sheet/sheet associations and the transition to a ribbon/tube morphology

Templating Molecular Arrays in Amyloid’s Cross-β Grooves

Amyloid fibers, independent of primary amino acid sequence, share a common cross-β structure and bind the histochemical dye Congo Red (CR). Despite extensive use of CR in amyloid diagnostics, remarkably little is known about the specific and characteristic binding interactions. Fibril insolubility, morphological inhomogeneity, and multiple possible ligand binding sites all conspire to limit characterization. Here, we have exploited the structure of cross-β nanotubes, which limit the number of potential binding sites, to directly interrogate cross-β laminate grooves. CR bound to cross-β nanotubes displays the hallmark apple-green interference color, a broad red-shifted low energy transition, and a Kd of 1.9 ± 0.5 μM. Oriented electron diffraction and linear dichroism defines the orientation of CR as parallel to the amyloid long axis and colinear with laminate grooves. The broad red-shifted UV signature of CR bound to amyloid can be explained by semiempirical quantum calculations that support the existence of a precise network of J- and H-CR aggregates, illuminating the ability of the amyloid to organize molecules into extended arrays that underlie the remarkable diagnostic potential of CR

DNA-Catalyzed Polymerization^†

Native DNA oligomers are shown to be stereoselective catalysts for the polymerization of 5‘-amino-3‘-acetaldehyde-modified thymidine/adenosine nucleosides through reductive amination. The reaction follows step-growth kinetics to read the encoded sequence and chain-length information in the antiparallel direction. Single mismatches in the template are selected against at a level of >100:1. A method is therefore established to translate biopolymer-encoded information stereoselectively into sequence- and chain-length specific synthetic polymers

Analysis of the Structure and Stability of a Backbone-Modified Oligonucleotide: Implications for Avoiding Product Inhibition in Catalytic Template-Directed Synthesis

The structural and thermodynamic origins of the destabilization of a backbone-modified DNA duplex 1, formed between d(CpGpTNTpGpC), containing a single aminoethyl group (−CH2−CH2−NH2+−) in place of the phosphodiester (−O−PO2-−O−) linkage of the central TT dimer, and d(GpCpApApCpG) are investigated. Analyses for the corresponding native duplex and two other related structural analogues of duplex 1 have been compared. Duplex 1 shows a cooperative thermal melting transition that is consistent with a two-state process. At a 2 mM concentration, the melting temperature of duplex 1 is reduced by 17 °C from the native duplex, and this decrease in stability is further assigned to an unfavorable decrease in enthalpy of 7 kcal mol-1 and a favorable increase in entropy of 15 eu mol-1. NMR structural analysis shows that the modified duplex 1 still adopts a canonical B-DNA conformation with Watson−Crick base pairing preserved; however, the CH2 group that replaces the native PO2- group in the modified backbone is flexible and free to collapse onto a hydrophobic core formed by the base edges and sugar rings of the flanking TT/AA nucleosides of the duplex. This conformation is significantly different from the maximally solvent-exposed orientation of the native phosphate in DNA. The entropic origin of the 15 eu mol-1 difference between the native and the modified duplex 1 is attributed to the hydrophobic interaction between the collapsed ethylamine linkage with the hydrophobic core of duplex 1. This assignment is further supported by a favorable comparison between the observed change in entropy and the estimated value for the hydrophobic interaction around the modified region. This estimated value is based on recent experimental measurement of the hydrophobic interaction between aliphatic groups and nucleic acids as well as ethylamine solvent transfer data. The overall decrease in the stability of duplex 1 results from a decrease in base stacking and hydrogen-bonding interactions between the base pairs. A model is, therefore, proposed to explain how the change in the local backbone conformation could disrupt the long-range cooperativity of DNA duplex formation upon backbone modifications. These studies provide an approach for identifying the factors that control the stability of the nucleic acid duplex structures containing backbone modifications, with direct implication for designing antisense oligonucleotides and template-directed reactions containing non-native phosphodiester linkages

Exploiting Amyloid Fibril Lamination for Nanotube Self-Assembly

Fundamental questions about the relative arrangement of the β-sheet arrays within amyloid fibrils remain central to both its structure and the mechanism of self-assembly. Recent computational analyses suggested that sheet-to-sheet lamination was limited by the length of the strand. On the basis of this hypothesis, a short seven-residue segment of the Alzheimer's disease-related Aβ peptide, Aβ(16−22), was allowed to self-assemble under conditions that maintained the basic amphiphilic character of Aβ. Indeed, the number increased over 20-fold to 130 laminates, giving homogeneous bilayer structures that supercoil into long robust nanotubes. Small-angle neutron scattering and X-ray scattering defined the outer and inner radii of the nanotubes in solution to contain a 44-nm inner cavity with 4-nm-thick walls. Atomic force microscopy and transmission electron microscopy images further confirmed these homogeneous arrays of solvent-filled nanotubes arising from a flat rectangular bilayer, 130 nm wide × 4 nm thick, with each bilayer leaflet composed of laminated β-sheets. The corresponding backbone H-bonds are along the long axis, and β-sheet lamination defines the 130-nm bilayer width. This bilayer coils to give the final nanotube. Such robust and persistent self-assembling nanotubes with positively charged surfaces of very different inner and outer curvature now offer a unique, robust, and easily accessible scaffold for nanotechnology

Dynamics and Fluidity of Amyloid Fibrils: A Model of Fibrous Protein Aggregates

A previous experimentally defined model for the fibril formed from the core residues of the β-amyloid (Aβ) peptides of Alzheimer's disease, 10YEVHHQKLVFFAEDVGSNKGAIIGLM, Aβ(10−35) using spectroscopic and scattering analyses reports on the average structure, benefiting immensely from the homogeneous assembly of Aβ(10−35). However, the energetic constraints that contribute to fibril dynamics and stability remain poorly understood. Here we perform molecular dynamics simulations to extend the structural assignment by providing evidence for a dynamic average ensemble with transient backbone H-bonds and internal solvation contributing to the inherent stability of amyloid fibrils

Dynamics and Fluidity of Amyloid Fibrils: A Model of Fibrous Protein Aggregates

A previous experimentally defined model for the fibril formed from the core residues of the β-amyloid (Aβ) peptides of Alzheimer's disease, 10YEVHHQKLVFFAEDVGSNKGAIIGLM, Aβ(10−35) using spectroscopic and scattering analyses reports on the average structure, benefiting immensely from the homogeneous assembly of Aβ(10−35). However, the energetic constraints that contribute to fibril dynamics and stability remain poorly understood. Here we perform molecular dynamics simulations to extend the structural assignment by providing evidence for a dynamic average ensemble with transient backbone H-bonds and internal solvation contributing to the inherent stability of amyloid fibrils