If liquids, polymers, bio-materials, metals and molten salts can avoid crystallization during cooling or compression, they freeze into a microscopically disordered solid-like state, a glass 1,2 . On approaching the glass transition, particles become trapped in transient cages-in which they rattle on picosecond timescales-formed by their nearest neighbours; the particles spend increasing amounts of time in their cages as the average escape time, or structural relaxation time τ α , increases from a few picoseconds to thousands of seconds through the transition. Owing to the huge difference between relaxation and vibrational timescales, theoretical 3-9 studies addressing the underlying rattling process have challenged our understanding of the structural relaxation. Numerical 10-13 and experimental studies on liquids 14 In the solid state atoms oscillate with mean square amplitude u 2 around their equilibrium positions (henceforth to be referred to as the Debye-Waller (DW) factor). With increasing temperature, solids meet different fates depending on the structural degree of order. In the crystalline state the ordered structure melts at T m , whereas in the amorphous state the disordered structure softens at the glass transition temperature T g , above which flow occurs with viscosity η. The empirical law T g 2/3T m (refs 1,2,7) suggests that the two phenomena have a common basis. In fact, this viewpoint motivated extensions to glasses 24 of the Lindemann melting criterion for crystalline solids 22 and pictures the glass transition as a freezing in an aperiodic crystal structure (ACS) 5 .According to the ACS model, the viscous flow is due to activated jumps over energy barriers E ∝ k B T a 2 / u 2 , where a is the displacement to overcome the barrier, k B is the Boltzmann constant and T the temperature. The usual rate theory leads to the Hall-Wolynes (HW) equation 5,21 τ α , η ∝ exp(a 2 /2 u 2 ). u 2 is the DW factor of the liquid, that is, it is the amplitude of the rattling motion within the cage of the surrounding atoms. This vibrational regime is assumed to occur on short timescales largely separated by those of the brownian diffusion. The ACS model is expected to fail when τ α becomes comparable to the typical rattling times corresponding to picosecond timescales, a condition that is met at high temperatures (for example, in selenium it occurs at T m + 104 K (ref. 14)).

Intrinsically disordered proteins (IDPs) are a unique class of proteins that have no stable native structure, a feature that allows them to adopt a wide variety of extended and compact conformations that facilitate a large number of vital physiological functions. One of the most well-known IDPs is the microtubule-associated tau protein, which regulates microtubule growth in the nervous system. However, dysfunctions in tau can lead to tau oligomerization, fibril formation, and neurodegenerative disease, including Alzheimer's disease. Using a combination of simulations and experiments, we explore the role of osmolytes in regulating the conformation and aggregation propensities of the R2/wt peptide, a fragment of tau containing the aggregating paired helical filament (PHF6*). We show that the osmolytes urea and trimethylamine N-oxide (TMAO) shift the population of IDP monomer structures, but that no new conformational ensembles emerge. Although urea halts aggregation, TMAO promotes the formation of compact oligomers (including helical oligomers) through a newly proposed mechanism of redistribution of water around the perimeter of the peptide. We put forth a "superposition of ensembles" hypothesis to rationalize the mechanism by which IDP structure and aggregation is regulated in the cell.protein folding | intrinsically disordered proteins | molecular dynamics simulations | osmolytes | tau protein M ost proteins in the human body have a well-defined, stable three-dimensional structure that is intimately tied to their physiological function. In the past few decades however, researchers have also identified a class of proteins that are natively unstructured. The latter, often referred to as intrinsically disordered proteins (IDPs) (1), are widespread and have the ability to quickly change their conformations to participate in a variety of biological processes. IDPs typically contain multiple charged side chains and few hydrophobic residues. Despite these characteristics, IDPs are not typically found in extended states but rather populate compact states due to hydrogen bonds and salt bridges (2, 3). IDP structures are highly regulated in the cell, and aberrant regulation often results in protein aggregation.In this paper we consider the effect of external agents, specifically osmolytes, in regulating IDP structure and aggregation properties. To carry out this study, we focused on the microtubule-associated protein tau, a soluble (4), archetypical IDP found in the nervous system that helps regulate and stabilize microtubules (5, 6). When the regulation of tau structure and activity is compromised, tau loses its ability to bind to microtubules, and disassociated tau proteins can aggregate into supramolecular assemblies with a cross-β structure (7-9) typical of amyloid fibers. This aggregation process is a pathological hallmark of Alzheimer's disease and other forms of dementia known as tauopathies (10, 11). We consider here a segment of tau, the R2/wt fragment 273 GKVQIINKKLDL 284 , which contains the highly aggregation ...

Self-aggregation of the microtubule-binding protein Tau reduces its functionality and is tightly associated with Tau-related diseases, termed tauopathies. Tau aggregation is also strongly associated with two nucleating six-residue segments, namely PHF6 (VQIVYK) and PHF6* (VQIINK). In this paper, using experiments and computational modeling, we study the self-assembly of individual and binary mixtures of Tau fragments containing PHF6* (R2/wt; 273GKVQIINKKLDL284) and PHF6 (R3/wt; 306VQIVYKPVDLSK317), and a mutant R2/ΔK280 associated with a neurodegenerative tauopathy. The initial stage of aggregation is probed by ion-mobility mass spectrometry, the kinetics of aggregation monitored with Thioflavin T assays and the morphology of aggregates visualized by transmission electron microscopy. Insights into the structure of early aggregates and the factors stabilizing the aggregates are obtained from replica exchange molecular dynamics simulations. Our data suggest that R3/wt has a much stronger aggregation propensity than either R2/wt or R2/ΔK280. Heterodimers containing R3/wt are less stable than R3/wt homodimers but much more stable than homodimers of R2/wt and R2/ΔK280, suggesting a possible role of PHF6*/PHF6 interactions in initiating the aggregation of full length Tau. Lastly, R2/ΔK280 binds stronger to R3/wt than R2/wt suggesting a possible mechanism for a pathological loss of normal Tau function.

The structural properties of water molecules surrounding TMAO molecules are studied using a newly developed atomistic force field for TMAO, combined with a multiscale coarse-graining (MS-CG) force field derived from the atomistic simulations. The all-atom force field is parametrized to work with the OPLS force field and with SPC, TIP3P, and TIP4P water models. The dual-resolution modeling enables a complete study of the dynamical and structural properties of the system, with the CG model providing important new physical insights into which interactions are critical in determining the structure of water around TMAO. TMAO is an osmolyte that stabilizes protein structures under conditions of chemical, thermal, and pressure denaturation. This molecule is excluded from the surface of proteins, and its effect on protein stability is mediated through TMAO-water interactions. We find that TMAO strongly binds two to three water molecules and, surprisingly, that methyl groups repel both the other methyl groups of TMAO and water molecules alike. The latter result is important because it shows that methyl groups are not interacting with each other through the expected hydrophobic effect (which would be attractive and not repulsive) and that the repulsion of water molecules forces a clathrate-like hydrogen bond network around them. We speculate that TMAO is excluded from the vicinity of the protein because the peculiar structure of water around TMAO prevents this molecule from coming in close contact with the protein.