Hydrophobic collapse overrides Coulombic repulsion in ferricytochrome c fibrillation under extremely alkaline condition

Anatomy of a selectively coassembled β-sheet peptide nanofiber

Peptide self-assembly, wherein molecule A associates with other A molecules to form fibrillar β-sheet structures, is common in nature and widely used to fabricate synthetic biomaterials. Selective coassembly of peptide pairs A and B with complementary partial charges is gaining interest due to its potential for expanding the form and function of biomaterials that can be realized. It has been hypothesized that charge-complementary peptides organize into alternating ABAB-type arrangements within assembled β-sheets, but no direct molecular-level evidence exists to support this interpretation. We report a computational and experimental approach to characterize molecular-level organization of the established peptide pair, CATCH. Discontinuous molecular dynamics simulations predict that CATCH(+) and CATCH(-) peptides coassemble but do not self-assemble. Two-layer β-sheet amyloid structures predominate, but off-pathway β-barrel oligomers are also predicted. At low concentration, transmission electron microscopy and dynamic light scattering identified nonfibrillar ∼20-nm oligomers, while at high concentrations elongated fibers predominated. Thioflavin T fluorimetry estimates rapid and near-stoichiometric coassembly of CATCH(+) and CATCH(-) at concentrations ≥100 μM. Natural abundance ¹³C NMR and isotope-edited Fourier transform infrared spectroscopy indicate that CATCH(+) and CATCH(-) coassemble into two-component nanofibers instead of self-sorting. However, ¹³C-¹³C dipolar recoupling solid-state NMR measurements also identify nonnegligible AA and BB interactions among a majority of AB pairs. Collectively, these results demonstrate that strictly alternating arrangements of β-strands predominate in coassembled CATCH structures, but deviations from perfect alternation occur. Off-pathway β-barrel oligomers are also suggested to occur in coassembled β-strand peptide systems.

Amyloid fibrillation of an intrinsically disordered plant phloem protein AtPP16-1 under acidic condition

Arabidopsis thaliana Phloem Protein 16-1 (AtPP16-1) is a 156-residue intrinsically disordered nucleic acid binding protein which is putatively involved in long-distance systemic transport of RNA to budding regions in plants. Dimerization or oligomerization of the protein at pH higher than about 4.1 leaves no apolar surface exposed for interaction with the dye 8-Anilinonaphthalene-1-sulfonate (ANS). The most stable monomeric state is found near pH 4 where the structure of the protein is determined to have three short β-strands and a single α-helix. By surveying the pH-dependent propensity of fibrillation we find the protein enters the amyloidogenic state at pH 2, 60 °C. The reaction product is not amorphous aggregate, but simple amyloid fibrils with sparse or no branching. The mean diameters of the fibril population scaled from AFM images are 13.2 and 21.2 nm for precursor aggregates (PA) and proto- or elongated fibrils, respectively. These values are somewhat larger than the fibril diameters generally cited, and the reason could be larger lateral association for both PA and protofibrils. The protein AtPP16-1 is strictly pH-selective in terms of its structure and stability, and the solution structure is known at pH 4. Under the conditions of pH 2 used here for fibrillation, the protein retains substantial secondary structure. Even if the pH and temperature conditions used for fibrillation are hardly physiological, there is a finite possibility that some aggregation of AtPP16-1 would occur in vivo, as the case of transglutaminase aggregates in the chloroplast of transplastomic plants, for example. The pH related problem has been discussed in detail, but the questions emanating are: do phloem proteins fibrillate in vivo, and if so what implication fibrillation has for plant physiology?

Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis

Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.

Kinetics of protein fibril formation: Methods and mechanisms

Amyloid fibril formation is a self-assembly reaction induced by favourable conformational changes of proteins leading to a stable, structurally organized aggregates. The deposition of stable protein fibrils in organs and tissues results in many diseases which are generally referred as amyloidosis. Though different disease conditions originate from sequentially and structurally different proteins, their fibrillar forms share common structural features. In vitro, fibril structure and kinetic pathway are investigated by using spectroscopic (fluorescence, circular dichroism, crystallography and solid state-NMR) and microscopic techniques. The kinetics of fibril formation is analysed using different mechanisms to understand the microscopic processes involved in the fibrillation reaction. This review discusses the assumptions, mechanisms, and limitations of some of the widely applied kinetic equations. Understanding of these equations would help to quantify the effect of the different microscopic process on the overall fibrillation kinetics which could aid in designing appropriate molecules to intervene in the aggregation process at different stages.

Copper(II) directs formation of toxic amorphous aggregates resulting in inhibition of hen egg white lysozyme fibrillation under alkaline salt-mediated conditions

Hen egg white lysozyme (HEWL) adopts a molten globule-like state at high pH (~12.75) and is found to form amyloid fibrils at alkaline pH. Here, we report that Cu(II) inhibits self-association of HEWL at pH 12.75 both at 37 and 65 °C. A significant reduction in Thioflavin T fluorescence intensity, attenuation in β-sheet content and reduction in hydrophobic exposure were observed with increasing Cu(II) stoichiometry. Electron paramagnetic resonance spectroscopy suggests a 4N type of coordination pattern around Cu(II) during fibrillation. Cu(II) is also capable of altering the cytotoxicity of the proteinaceous aggregates. Fibrillar species of diverse morphology were found in the absence of Cu(II) with the generation of amorphous aggregates in the presence of Cu(II), which are more toxic compared to the fibrils alone.