Transient isomers in the photodissociation of bromoiodomethane.

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 µs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

Water/ice phase transition: The role of zirconium acetate, a compound with ice-shaping properties.

Few compounds feature ice-shaping properties. Zirconium acetate is one of the very few inorganic compounds reported so far to have ice-shaping properties similar to that of ice-shaping proteins, encountered in many organisms living at low temperature. When a zirconium acetate solution is frozen, oriented and perfectly hexagonal ice crystals can be formed and their growth follows the temperature gradient. To shed light on the water/ice phase transition while freezing zirconium acetate solution, we carried out differential scanning calorimetry measurements. From our results, we estimate how many water molecules do not freeze because of their interaction with Zr cations. We estimate the colligative properties of the Zr acetate on the apparent critical temperature. We further show that the phase transition is unaffected by the nature of the base which is used to adjust the pH. Our results provide thus new hints on the ice-shaping mechanism of zirconium acetate.

Polyproline as a Minimal Antifreeze Protein Mimic That Enhances the Cryopreservation of Cell Monolayers.

Tissue engineering, gene therapy, drug screening, and emerging regenerative medicine therapies are fundamentally reliant on high-quality adherent cell culture, but current methods to cryopreserve cells in this format can give low cell yields and require large volumes of solvent "antifreezes". Herein, we report polyproline as a minimum (bio)synthetic mimic of antifreeze proteins that is accessible by solution, solid-phase, and recombinant methods. We demonstrate that polyproline has ice recrystallisation inhibition activity linked to its amphipathic helix and that it enhances the DMSO cryopreservation of adherent cell lines. Polyproline may be a versatile additive in the emerging field of macromolecular cryoprotectants.

Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion.

Among the various biophysical methods available to investigate protein dynamics, NMR presents the ability to scrutinize protein motions on a broad range of time scales. 1H-15N NMR spin relaxation experiments can reveal the extent of protein motions across the picosecond-nanosecond dynamics probed by the fundamental parameters 15N-R1, 15N-R2, and 1H-15N NOE that can be well sampled by molecular dynamics (MD) simulations. An accurate prediction of these parameters is subjected to a proper description of the rotational diffusion and anisotropy. Indeed, a strong rotational anisotropy has a profound effect on the various relaxation parameters and could be mistaken for conformational exchange. Although the principle of NMR spin relaxation predictions from MD is now well established, numerous NMR/MD comparisons have hitherto focused on proteins that show low to moderate anisotropy and make use of a scaling factor to remove artifacts arising from water model-dependence of the rotational diffusion. In the present work, we have used NMR to characterize the rotational diffusion of the α-helical STAM2-UIM domain by measuring the 15N-R1, 15N-R2, and 1H-15N NOE relaxation parameters. We therefore highlight the use of the polarizable AMOEBA force field (FF) and show that it improves the prediction of the rotational diffusion in the particular case of strong rotational anisotropy, which in turn enhances the prediction of the 15N-R1, 15N-R2, and 1H-15N NOE relaxation parameters without the requirement of a scaling factor. Our findings suggest that the use of polarizable FFs could potentially enrich our understanding of protein dynamics in situations where charge distribution or protein shape is remodeled over time like in the case of multidomain proteins or intrinsically disordered proteins.

Dimensionality crossover in the induced magnetization of Pd layers.

The magnetic ordering of a series of samples consisting of ultrathin Fe layers embedded in Pd was investigated using the magneto-optical Kerr effect. The samples consisted of a single Fe layer with nominal thickness 0.2≤d(Fe)≤1.6 monolayers sandwiched between two 20 monolayer Pd layers. A dimensionality crossover from two dimensions to three dimensions occurs as d(Fe) is increased from 0.4 to 1.0 monolayers. First-principles calculations were performed in order to determine the magnetic profile, and we used a spin-wave quantum well model for obtaining a qualitative description of the dimensionality crossover. The results clearly prove the existence of a dimensionality crossover in the induced magnetization, opening new routes for addressing the influence of extension on order.

Time-Lapse, in Situ Imaging of Ice Crystal Growth Using Confocal Microscopy.

Ice crystals nucleate and grow when a water solution is cooled below its freezing point. The growth velocities and morphologies of the ice crystals depend on many parameters, such as the temperature of ice growth, the melting temperature, and the interactions of solutes with the growing crystals. Three types of morphologies may appear: dendritic, cellular (or fingerlike), or the faceted equilibrium form. Understanding and controlling which type of morphology is formed is essential in several domains, from biology to geophysics and materials science. Obtaining, in situ, three dimensional observations without introducing artifacts due to the experimental technique is nevertheless challenging. Here we show how we can use laser scanning confocal microscopy to follow in real-time the growth of smoothed and faceted ice crystals in zirconium acetate solutions. Both qualitative and quantitative observations can be made. In particular, we can precisely measure the lateral growth velocity of the crystals, a measure otherwise difficult to obtain. Such observations should help us understand the influence of the parameters that control the growth of ice crystals in various systems.

Deciphering solution scattering data with experimentally guided molecular dynamics simulations.

Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Dimensionality and confinement effects in δ-doped Pd(Fe) layers.

We address the dimensionality aspects of the magnetic ordering in δ-doped Pd(Fe) structures. The key property we investigate, via magneto-optic Kerr measurements, is the magnetization induced by iron in palladium, over a wide temperature range 5 K < T < 300 K. The dimensional crossover we observe cannot be rationalized on the basis of structural considerations alone, since we find the dimensionality of the low temperature and of the critical region can differ. We discuss the crossover in terms of the temperature dependence of the magnon modes, giving rise to lower dimensionality at low temperatures.