Labile assembly of a tardigrade protein induces biostasis

Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self-assembly of labile CAHS gels.

Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration

Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.

The slow Arrhenius process in small organic molecules

Equilibration, the complex set of molecular rearrangements leading to more stable states, is usually dominated by density fluctuations, occurring through the structural (α-)relaxation, whose timescale quickly increases upon cooling. Growing evidence shows, however, that equilibration can be reached also through an alternative pathway provided by the Slow Arrhenius process (SAP), a molecular mode slower than the structural processes in the liquid state and faster in glass. The SAP, widely observed in polymers, has not yet been reported in small molecules, probably because of the larger experimental difficulties in handling these systems. Here, we report the presence of the SAP in three different molecular glassformers, by investigating these systems in the thin film geometry via dielectric spectroscopy. These results reinforce the idea that the SAP is a universal feature of liquid and glassy dynamics.

Nanoconfined Water Clusters in Zinc White Oil Paint

Pigments in oil paint are bound by a complex oil polymer network that is prone to water-related chemical degradation. We use cryo-Fourier-transform infrared spectroscopy and differential scanning calorimetry to study how water distributes inside zinc white oil paint. By measuring water freezing and melting transitions, we show that water-saturated zinc white oil paint contains both liquid-like clustered water and nonclustered water. A comparison of titanium white paint and nonpigmented model systems indicates that water clustering happens near the pigment-polymer interface. The cluster size was estimated in the nanometer range based on the ice melting and freezing temperatures and on the position of the O-D vibration band. As liquid-like water can play a crucial role in the dissolution and transport of ions and molecules, understanding the factors that favor this phenomenon is essential for establishing safe conditions for the conservation of painted works of art.

Raman Diffusion-Ordered Spectroscopy

The Stokes-Einstein relation, which relates the diffusion coefficient of a molecule to its hydrodynamic radius, is commonly used to determine molecular sizes in chemical analysis methods. Here, we combine the size sensitivity of such diffusion-based methods with the structure sensitivity of Raman spectroscopy by performing Raman diffusion-ordered spectroscopy (Raman-DOSY). The core of the Raman-DOSY setup is a flow cell with a Y-shaped channel containing two inlets: one for the sample solution and one for the pure solvent. The two liquids are injected at the same flow rate, giving rise to two parallel laminar flows in the channel. After the flow stops, the solute molecules diffuse from the solution-filled half of the channel into the solvent-filled half at a rate determined by their hydrodynamic radius. The arrival of the solute molecules in the solvent-filled half of the channel is recorded in a spectrally resolved manner by Raman microspectroscopy. From the time series of Raman spectra, a two-dimensional Raman-DOSY spectrum is obtained, which has the Raman frequency on one axis and the diffusion coefficient (or equivalently, hydrodynamic radius) on the other. In this way, Raman-DOSY spectrally resolves overlapping Raman peaks arising from molecules of different sizes. We demonstrate Raman-DOSY on samples containing up to three compounds and derive the diffusion coefficients of small molecules, proteins, and supramolecules (micelles), illustrating the versatility of Raman-DOSY. Raman-DOSY is label-free and does not require deuterated solvents and can thus be applied to samples and matrices that might be difficult to investigate with other diffusion-based spectroscopy methods.

Multidimensional Infrared Diffusion-Ordered Spectroscopy in depletion mode distinguishes protein amyloids and monomers

Conventional and two-dimensional infrared (2D-IR) spectroscopy are well suited to study amyloid aggregates, because the amide I mode is a sensitive probe of the aggregate structure. However, these methods are not so useful to study mixtures of aggregates and monomers, which generally have overlapping amide I spectra. Here, we show that IR-Diffusion-Ordered Spectroscopy (IR-DOSY) can disentangle the contributions of protein monomers and aggregates in FTIR and 2D-IR spectra by separating the spectral contributions based on molecular size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient inside an infrared sample cell and tracking its equilibration in an IR-frequency resolved manner. The protein-aggregate diffusion is too slow to be experimentally observable, so instead of tracking the arrival of molecular species diffusing into the initially empty region of the sample cell, we track the depletion of the more rapidly diffusing species as they leave the sample-filled region. In this way, we can still obtain the spectrum of very slowly diffusing species, although we cannot determine their diffusion coefficient. We first demonstrate this depletion method on a mixture of two small organic molecules, and then show how it can be used to separate the spectrum of a mixture of bovine-serum-albumin amyloids and monomers into its component spectra, both in the FTIR and 2D-IR case.

Hydrogen Bonds under Stress: Strain-Induced Structural Changes in Polyurethane Revealed by Rheological Two-Dimensional Infrared Spectroscopy

The remarkable elastic properties of polymers are ultimately due to their molecular structure, but the relation between the macroscopic and molecular properties is often difficult to establish, in particular for (bio)polymers that contain hydrogen bonds, which can easily rearrange upon mechanical deformation. Here we show that two-dimensional infrared spectroscopy on polymer films in a miniature stress tester sheds new light on how the hydrogen-bond structure of a polymer is related to its viscoelastic response. We study thermoplastic polyurethane, a block copolymer consisting of hard segments of hydrogen-bonded urethane groups embedded in a soft matrix of polyether chains. The conventional infrared spectrum shows that, upon deformation, the number of hydrogen bonds increases, a process that is largely reversible. However, the 2DIR spectrum reveals that the distribution of hydrogen-bond strengths becomes slightly narrower after a deformation cycle, due to the disruption of weak hydrogen bonds, an effect that could explain the strain-cycle induced softening (Mullins effect) of polyurethane. These results show how rheo-2DIR spectroscopy can bridge the gap between the molecular structure and the macroscopic elastic properties of (bio)polymers.

Extreme ultraviolet transient gratings: A tool for nanoscale photoacoustics

Collective lattice dynamics determine essential aspects of condensed matter, such as elastic and thermal properties. These exhibit strong dependence on the length-scale, reflecting the marked wavevector dependence of lattice excitations. The extreme ultraviolet transient grating (EUV TG) approach has demonstrated the potential of accessing a wavevector range corresponding to the 10s of nm length-scale, representing a spatial scale of the highest relevance for fundamental physics and forefront technology, previously inaccessible by optical TG and other inelastic scattering methods. In this manuscript we report on the capabilities of this technique in the context of probing thermoelastic properties of matter, both in the bulk and at the surface, as well as discussing future developments and practical considerations.

Infrared Diffusion-Ordered Spectroscopy Reveals Molecular Size and Structure

Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.

In Situ Identification of Secondary Structures in Unpurified Bombyx mori Silk Fibrils Using Polarized Two-Dimensional Infrared Spectroscopy

The mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behavior of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the noninvasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools because the absorption bands of amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk films cast from Bombyx mori silk feedstock. Without any additional peak fitting, we find that the initial effect of hydration is an increase of the random coil content at the expense of the helical content, while the β-sheet content is unchanged and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.

Fluorescent molecular rotor probes nanosecond viscosity changes

Viscosity is a key property of liquids, but it is difficult to measure in short-lived, metastable samples due to the long measuring times required by conventional rheology. Here, we show how this problem can be solved by using fluorescent molecular rotors. The excited-state fluorescence decay rate of these molecules is sensitive to the viscosity of their local environment, and by combining pulsed laser excitation with time-resolved fluorescence detection, we can measure viscosities with a time resolution of a few ns. We demonstrate this by measuring in real time the viscosity change in glycerol induced by a nanosecond temperature jump. This new approach makes it possible to measure the viscosity of extremely short-lived states of matter.

Lifetime-Associated Two-Dimensional Infrared Spectroscopy Reveals the Hydrogen-Bond Structure of Supercooled Water in Soft Confinement

We demonstrate a method to address the problem of spectral overlap in multidimensional vibrational spectroscopy and use it to investigate supercooled aqueous sorbitol solutions. The absence of crystallization in these solutions has been attributed to "soft" confinement of water in subnanometer voids in the sorbitol matrix, but the details of the hydrogen-bond structure are still largely unknown. 2D-IR spectroscopy of the OH-stretch mode is an excellent tool to investigate hydrogen bonding, but in this case it seems difficult because of the overlapping water and sorbitol contributions to the 2D-IR spectrum. Using the difference in OH-stretch lifetimes of water and sorbitol we can cleanly separate these contributions. Surprisingly, the separated 2D-IR spectra show that the hydrogen-bond disorder of soft-confined water is independent of temperature and decoupled from its orientational order. We believe the approach we use to separate overlapping 2D-IR spectra will enhance the applicability of 2D-IR spectroscopy to study multicomponent systems.

Experimental evidence of mosaic structure in strongly supercooled molecular liquids

When a liquid is cooled to produce a glass its dynamics, dominated by the structural relaxation, become very slow, and at the glass-transition temperature T_g its characteristic relaxation time is about 100 s. At slightly elevated temperatures (~1.2 T_g) however, a second process known as the Johari-Goldstein relaxation, β_JG, decouples from the structural one and remains much faster than it down to T_g. While it is known that the β_JG-process is strongly coupled to the structural relaxation, its dedicated role in the glass-transition remains under debate. Here we use an experimental technique that permits us to investigate the spatial and temporal properties of the β_JG relaxation, and give evidence that the molecules participating in it are highly mobile and spatially connected in a system-spanning, percolating cluster. This correlation of structural and dynamical properties provides strong experimental support for a picture, drawn from theoretical studies, of an intermittent mosaic structure in the deeply supercooled liquid phase.

The Johari-Goldstein relaxation is a precursor of the glass transition in liquids. Caporaletti et al. use time-dependent interferometry data to substantiate its suggested structural appearance as a globally percolating, fluctuating mosaic.

Microscopic pathways for stress relaxation in repulsive colloidal glasses

Residual stresses are well-known companions of all glassy materials. They affect and, in many cases, even strongly modify important material properties like the mechanical response and the optical transparency. The mechanisms through which stresses affect such properties are, in many cases, still under study, and their full understanding can pave the way to a full exploitation of stress as a primary control parameter. It is, for example, known that stresses promote particle mobility at small length scales, e.g., in colloidal glasses, gels, and metallic glasses, but this connection still remains essentially qualitative. Exploiting a preparation protocol that leads to colloidal glasses with an exceptionally directional built-in stress field, we characterize the stress-induced dynamics and show that it can be visualized as a collection of "flickering," mobile regions with linear sizes of the order of ≈20 particle diameters (≈2 μm here) that move cooperatively, displaying an overall stationary but locally ballistic dynamics.

A microscopic look at the Johari-Goldstein relaxation in a hydrogen-bonded glass-former

Understanding the glass transition requires getting the picture of the dynamical processes that intervene in it. Glass-forming liquids show a characteristic decoupling of relaxation processes when they are cooled down towards the glassy state. The faster (βJG) process is still under scrutiny, and its full explanation necessitates information at the microscopic scale. To this aim, nuclear γ-resonance time-domain interferometry (TDI) has been utilized to investigate 5-methyl-2-hexanol, a hydrogen-bonded liquid with a pronounced βJG process as measured by dielectric spectroscopy. TDI probes in fact the center-of-mass, molecular dynamics at scattering-vectors corresponding to both inter- and intra-molecular distances. Our measurements demonstrate that, in the undercooled liquid phase, the βJG relaxation can be visualized as a spatially-restricted rearrangement of molecules within the cage of their closest neighbours accompanied by larger excursions which reach out at least the inter-molecular scale and are related to cage-breaking events. In-cage rattling and cage-breaking processes therefore coexist in the βJG relaxation.

Nanoscale transient gratings excited and probed by extreme ultraviolet femtosecond pulses

Advances in developing ultrafast coherent sources operating at extreme ultraviolet (EUV) and x-ray wavelengths allow the extension of nonlinear optical techniques to shorter wavelengths. Here, we describe EUV transient grating spectroscopy, in which two crossed femtosecond EUV pulses produce spatially periodic nanoscale excitations in the sample and their dynamics is probed via diffraction of a third time-delayed EUV pulse. The use of radiation with wavelengths down to 13.3 nm allowed us to produce transient gratings with periods as short as 28 nm and observe thermal and coherent phonon dynamics in crystalline silicon and amorphous silicon nitride. This approach allows measurements of thermal transport on the ~10-nm scale, where the two samples show different heat transport regimes, and can be applied to study other phenomena showing nontrivial behaviors at the nanoscale, such as structural relaxations in complex liquids and ultrafast magnetic dynamics.

A new experimental scheme for nuclear γ-resonance time-domain interferometry

Time-domain interferometry (TDI) based on nuclear resonant scattering of synchrotron radiation by Mössbauer nuclei is a promising technique to study slow dynamics at the interatomic length scale. In order to improve the efficiency of this technique, a new TDI scheme is developed involving the use of a nuclear absorber with a two-line energy spectrum combined with a single-line spectrum. Different from other TDI setups, the issue of external vibrations is much reduced since the two absorbers are at rest and no velocity transducer is used. This allows measuring beating patterns with satisfying statistical accuracy and contrast up to 350 ns. We report here the characterization of the experimental setup necessary for the implementation of this new scheme. The model required for the description of the beating pattern produced by a three-line spectrum system is also discussed in detail. Finally, we report some results for the dynamics of the prototypical glass-former ortho-terphenyl to demonstrate the possibilities offered by this new scheme.