Michaela Zamponi

Neutron scattering reveals extremely slow cell water in a Dead Sea organism

Intracellular water dynamics in Haloarcula marismortui, an extremely halophilic organism originally isolated from the Dead Sea, was studied by neutron scattering. The water in centrifuged cell pellets was examined by means of two spectrometers, IN6 and IN16, sensitive to motions with time scales of 10 ps and 1 ns, respectively. From IN6 data, a translational diffusion constant of 1.3 × 10−5 cm2 s−1 was determined at 285 K. This value is close to that found previously for other cells and close to that for bulk water, as well as that of the water in the 3.5 M NaCl solution bathing the cells. A very slow water component was discovered from the IN16 data. At 285 K the water-protons of this component displays a residence time of 411 ps (compared with a few ps in bulk water). At 300 K, the residence time dropped to 243 ps and was associated with a translational diffusion of 9.3 × 10−8 cm2 s−1, or 250 times lower than that of bulk water. This slow water accounts for ≈76% of cell water in H. marismortui. No such water was found in Escherichia coli measured on BSS, a neutron spectrometer with properties similar to those of IN16. It is hypothesized that the slow mobility of a large part of H. marismortui cell water indicates a specific water structure responsible for the large amounts of K+ bound within these extremophile cells.

Hydration water mobility is enhanced around tau amyloid fibers

Significance Protein aggregation into amyloid fibers and oligomers is observed in a variety of neurodegenerative diseases. The fibers formed by the intrinsically disordered human protein tau, for instance, are one of the hallmarks of Alzheimer disease. In this work, we report on the dynamic behavior of tau hydration water, which we found to be more mobile in tau fibers than in nonaggregated tau. This increase in mobility could promote fiber formation through an increase in hydration water entropy. That hydration water is more mobile around the pathological form of tau corroborates that methodologies sensitive to the diffusion of water, such as diffusion magnetic resonance imaging, could be used to diagnose Alzheimer patients in an early stage of the disease. The paired helical filaments (PHF) formed by the intrinsically disordered human protein tau are one of the pathological hallmarks of Alzheimer disease. PHF are fibers of amyloid nature that are composed of a rigid core and an unstructured fuzzy coat. The mechanisms of fiber formation, in particular the role that hydration water might play, remain poorly understood. We combined protein deuteration, neutron scattering, and all-atom molecular dynamics simulations to study the dynamics of hydration water at the surface of fibers formed by the full-length human protein htau40. In comparison with monomeric tau, hydration water on the surface of tau fibers is more mobile, as evidenced by an increased fraction of translationally diffusing water molecules, a higher diffusion coefficient, and increased mean-squared displacements in neutron scattering experiments. Fibers formed by the hexapeptide 306VQIVYK311 were taken as a model for the tau fiber core and studied by molecular dynamics simulations, revealing that hydration water dynamics around the core domain is significantly reduced after fiber formation. Thus, an increase in water dynamics around the fuzzy coat is proposed to be at the origin of the experimentally observed increase in hydration water dynamics around the entire tau fiber. The observed increase in hydration water dynamics is suggested to promote fiber formation through entropic effects. Detection of the enhanced hydration water mobility around tau fibers is conjectured to potentially contribute to the early diagnosis of Alzheimer patients by diffusion MRI.

Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution

The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.

Structure and Dynamics of a Compact State of a Multidomain Protein, the Mercuric Ion Reductase

The functional efficacy of colocalized, linked protein domains is dependent on linker flexibility and system compaction. However, the detailed characterization of these properties in aqueous solution presents an enduring challenge. Here, we employ a novel, to our knowledge, combination of complementary techniques, including small-angle neutron scattering, neutron spin-echo spectroscopy, and all-atom molecular dynamics and coarse-grained simulation, to identify and characterize in detail the structure and dynamics of a compact form of mercuric ion reductase (MerA), an enzyme central to bacterial mercury resistance. MerA possesses metallochaperone-like N-terminal domains (NmerA) tethered to its catalytic core domain by linkers. The NmerA domains are found to interact principally through electrostatic interactions with the core, leashed by the linkers so as to subdiffuse on the surface over an area close to the core C-terminal Hg(II)-binding cysteines. How this compact, dynamical arrangement may facilitate delivery of Hg(II) from NmerA to the core domain is discussed.

Photoactivation Reduces Side-Chain Dynamics of a LOV Photoreceptor

We used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (LOV) photoreceptor PpSB1-LOV from Pseudomonas putida in both the dark and light states. Global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. Global protein diffusion of PpSB1-LOV is not influenced by photoactivation. Observation-time-dependent global diffusion coefficients were found, which converge on the nanosecond timescale toward diffusion coefficients determined by dynamic light scattering. Mean-square displacements of localized internal motions and effective force constants, , describing the resilience of the proteins were determined on the respective timescales. Photoactivation significantly modifies the flexibility and the resilience of PpSB1-LOV. On the fast, picosecond timescale, small changes in the mean-square displacement and are observed, which are enhanced on the slower, nanosecond timescale. Photoactivation results in a slightly larger resilience of the photoreceptor on the fast, picosecond timescale, whereas in the nanosecond range, a significantly less resilient structure of the light-state protein is observed. For a residue-resolved interpretation of the experimental neutron-scattering data, we analyzed molecular dynamics simulations of the PpSB1-LOV X-ray structure. Based on these data, it is tempting to speculate that light-induced changes in the protein result in altered side-chain mobility mostly for residues on the protruding Jα helix and on the LOV-LOV dimer interface. Our results provide strong experimental evidence that side-chain dynamics play a crucial role in photoactivation and signaling of PpSB1-LOV via modulation of conformational entropy.

The Role of the Functionality in the Branch Point Motion in Symmetric Star Polymers: A Combined Study by Simulations and Neutron Spin Echo Spectroscopy

We investigate the effect of the number of arms (functionality f) on the mobility of the branch point in symmetric star polymers. For this purpose we carry out large-scale molecular dynamics simulations of simple bead–spring stars and neutron spin echo (NSE) spectroscopy experiments on center labeled polyethylene stars. This labeling scheme unique to neutron scattering allows us to directly observe the branch point motion on the molecular scale by measuring the dynamic structure factor. We investigate the cases of different functionalities f = 3, 4, and 5 for different arm lengths. The analysis of the branch point fluctuations reveals a stronger localization with increasing functionality, following 2/f scaling. The dynamic structure factors of the branch point are analyzed in terms of a modified version, incorporating dynamic tube dilution (DTD), of the Vilgis–Boue model for cross-linked networks [J. Polym. Sci., Part B 1988, 26, 2291−2302]. In DTD the tube parameters are renormalized with the tube surviv...

Thermodiffusion as a probe of protein hydration for streptavidin and the streptavidin-biotin complex

Molecular recognition via protein–ligand interactions is of fundamental importance to numerous processes in living organisms. Microscale thermophoresis (MST) uses the sensitivity of the thermophoretic response upon ligand binding to access information on the reaction kinetics. Additionally, thermophoresis is promising as a tool to gain information on the hydration layer, as the temperature dependence of the thermodiffusion behaviour is sensitive to solute-solvent interactions. To quantify the influence of structural fluctuations and conformational motion of the protein on the entropy change of its hydration layer upon ligand binding, we combine quasi-elastic incoherent neutron scattering (QENS) and isothermal titration calorimetry (ITC) data from literature. However, preliminary results show that replacing water with deuterated water leads to changes of the thermophoretic measurements, which are similar to the changes observed upon binding by biotin. In order to gain a better understanding of the hydratio...

Prompt γ radiation measured with a Nal scintillation detector: a beam monitor for neutron scattering instruments which needs no space in the beam

We investigate the possibility of using the prompt γ rays emitted by aluminum windows in order to monitor the neutron flux of the beam. A Nal scintillation detector is used to detect the prompt γ rays. No additional material apart from the unavoidable Al windows along the flight path is placed in the beam. The performance of the monitor is compared to that of a standard BF3-monitor placed in the beam. Influences of a magnetic field on the photomultiplier of the Nal monitor is discussed, as well as the influence of activation gammas. At an instrument using a beam chopper the time behaviour is discussed.