Distinguishing amyloid fibril structures in Alzheimer's disease (AD) by two-dimensional ultraviolet (2DUV) spectroscopy

Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study

Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.

Dual effect of 2D WS2 nanoparticles on the lysozyme conformation

In the present work we studied the effect of 2D WS₂ nanoparticles on the conformational changes in lysozyme protein at different pH values (2.0-11.5). The contributions of various structural conformations (α-helix, β-sheets parallel and antiparallel, unordered structure and side groups) were determined by decomposition of Amid I absorbance bands. The 2D WS₂ were shown to have different impact on secondary structure depending on pH of the solution and protein concentration. The amyloid fibril presence was confirmed with confocal microscopy enhanced by gold support, and fluorescent spectroscopy with amyloid-sensitive dye Thioflavin T. Our data show that WS₂ can both inhibit and stimulate amyloid formation. Additionally, we have also reported an unusual spectroscopic behavior displayed by lysozyme, indicated by narrowing of Amide I and Amide II bands at pH 2.5 and 3.5 when incubated with 2D WS2 nanoparticles.

Study of the γD-crystallin protein using two-dimensional infrared (2DIR) spectroscopy: experiment and simulation

Cataracts is a misfolding protein disease in which one of the major components is the γD-crystallin protein. The conformational structure of the aggregated γD-crystallin and the interactions that cause aggregation are largely unknown. A recent experimental two-dimensional infrared (2DIR) spectroscopy study determined that the C-terminal domain has a high propensity to form β-sheets whereas the N-terminal domain forms a disordered structure in the fiber state. We present a combined computational molecular dynamics and infrared spectroscopy study of the local dynamics of these domains. The computed 2DIR signals agree remarkably well with experiment. We show that the two domains, both of which have a Greek key structural fold, experience different electrostatic environments, which may be related to the fact that the C-terminal domain is more structurally stable than the N-terminal domain. We correlate the vibrational couplings to known energy dissipation mechanisms and reveal their origin.

Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy

Protein folding is one of the most fundamental problems in modern molecular biology. Uncovering the detailed folding mechanism requires methods that can monitor the structures at high temporal and spatial resolution. Two-dimensional infrared (2DIR) spectroscopy is a new tool for studying protein structures and dynamics with high time resolution. Using atomistic molecular dynamics simulations, we illustrate the folding process of Trp-cage along the dominant pathway on the free energy landscape by analyzing nonchiral and chiral coherent 2DIR spectra along the pathway. Isotope labeling is used to reveal residue-specific information. We show that the high resolution structural sensitivity of 2DIR can differentiate the ensemble evolution of protein and thus provides a microscopic picture of the folding process.

Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of plaque deposits in the human brain. The main component of these plaques consists of highly ordered structures called amyloid fibrils, formed by the amyloid β-peptide (Aβ). The mechanism connecting Aβ and AD is yet undetermined. In a previous study, a coarse-grained united-residue model and molecular dynamics simulations were used to model the growth mechanism of Aβ amyloid fibrils. On the basis of these simulations, a dock/lock mechanism was proposed, in which Aβ fibrils grow by adding monomers at either end of an amyloid fibril template. To examine the structures in the early time-scale formation and growth of amyloid fibrils, simulated two-dimensional ultraviolet spectroscopy is used. These early structures are monitored in the far ultraviolet regime (λ = 190-250 nm) in which the computed signals originate from the backbone nπ* and ππ* transitions. These signals show distinct cross-peak patterns that can be used, in combination with molecular dynamics, to monitor local dynamics and conformational changes in the secondary structure of Aβ-peptides. The protein geometry-correlated chiral xxxy signal and the non-chiral combined signal xyxy-xyyx were found to be sensitive to, and in agreement with, a dock/lock pathway.