Michler's hydrol blue elucidates structural differences in prion strains.

Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler's hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs.

Orientation of aromatic residues in amyloid cores: structural insights into prion fiber diversity.

Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.

Spectroscopic characterization of Coomassie blue and its binding to amyloid fibrils.

Coomassie brilliant blue G-250 (CB) is the dye used frequently in the Bradford assay for protein concentration determination. In this study, we investigated how the solvent polarity and viscosity affect the CB absorption and fluorescence spectra and apply this understanding to investigate the binding of CB to lysozyme and insulin in the native and amyloid fibril states. Coomassie blue binds both to the native protein and to amyloid fibrils but gives distinctly different spectral responses. The absorption and fluorescence spectra of CB indicate that binding sites in the fibrils are less polar and hold the CB dye more rigidly than in the native forms. The spectral comparison of CB bound to the two different fibrils showed that the binding sites are different, and this was most likely due to differences in secondary structure as monitored by circular dichroism. Finally, linear dichroism was used to show that the fibril-bound CB is oriented preferentially parallel to the insulin amyloid fibril axis.

A new highly adaptable design of shear-flow device for orientation of macromolecules for Linear Dichroism (LD) measurement.

This article presents a new design of flow-orientation device for the study of bio-macromolecules, including DNA and protein complexes, as well as aggregates such as amyloid fibrils and liposome membranes, using Linear Dichroism (LD) spectroscopy. The design provides a number of technical advantages that should make the device inexpensive to manufacture, easier to use and more reliable than existing techniques. The degree of orientation achieved is of the same order of magnitude as that of the commonly used concentric cylinders Couette flow cell, however, since the device exploits a set of flat strain-free quartz plates, a number of problems associated with refraction and birefringence of light are eliminated, increasing the sensitivity and accuracy of measurement. The device provides similar shear rates to those of the Couette cell but is superior in that the shear rate is constant across the gap. Other major advantages of the design is the possibility to change parts and vary sample volume and path length easily and at a low cost.

Michler's hydrol blue: a sensitive probe for amyloid fibril detection.

Michler's hydrol blue (MHB) is investigated with respect to photophysical properties in varied solvent environment and when bound to insulin and lysozyme fibrils. The MHB chromophore is shown to act like a molecular rotor and bind well to amyloid fibrils, where it exhibits a characteristic red-shift in its excitation spectrum and an increase in the emission quantum yield upon binding. MHB is more sensitive to environmental changes than Thioflavin T (ThT) and furthermore, in contrast to the latter amyloid probe, can differentiate between insulin and lysozyme fibrils by a more red-shifted excitation spectrum for insulin fibrils. To support the experimental observations, time-dependent density functional theory (TDDFT) calculations were performed on MHB at several levels of theory. The predicted changes of spectral properties as a function of the environment are in good agreement with the experimental results. Linear dichroism (LD) is used to determine the orientation of the MHB within the fibrils. It was shown through LD and molecular modeling that MHB aligns itself preferentially parallel with the amyloid fiber at an angle of 14°-22° to the fibril axis and along the grooves of the ß-sheet.

A spectroscopic study of 2-[4'-(dimethylamino)phenyl]-benzothiazole binding to insulin amyloid fibrils.

The spectroscopic properties of 2-[4'-(dimethylamino)phenyl]-benzothiazole (BTA-2) in solution and in the presence of amyloid fibrils were investigated using absorption and fluorescence spectroscopy. Solution studies show that BTA-2 forms micelles in aqueous solutions, but that the dye can be solvated upon the addition of acetonitrile (CH(3)CN). BTA-2 binds to amyloid fibrils in solution leading to a characteristic blue-shift in the emission spectrum and an increase in fluorescence intensity. However, in solutions with increasing CH(3)CN concentration, there was a marked decrease in binding of the BTA-2 to fibrils. Studies demonstrating the effect of BTA-2 concentration on binding were performed. A comparison with the standard amyloid fluorescent marker, thioflavin T (ThT), showed that BTA-2 is more fluorescent, making it an excellent dye to label amyloid samples.

Near-field scanning optical microscopy measurements of fluorescent molecular probes binding to insulin amyloid fibrils.

The binding of two amyloid fibril stain dyes, thioflavin T (ThT) and its neutral analog 2-[4'-(dimethylamino)phenyl]-benzothiazole (BTA-2), are measured using near-field scanning optical microscopy (NSOM), which is able to image individual amyloid fibrils. Polarized NSOM images reveal that both dyes bind to the fibrils with the long axis of the molecule aligned parallel to the long axis of the fibrils. This indicates that the dyes bind along the surface of the beta-sheet within the grooves of the fibril that run parallel to the fibril axis. The similarity in the binding motifs of the two dyes shows that electrostatic interaction of the charged amine group on the ThT dye plays a minimal role in the affinity of the dyes for the amyloids. The polarized NSOM images confirm that the enhanced fluorescence of the ThT and BTA-2 result from binding of the monomeric dye rather than micelles or excimer species.