Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase.

Guanylate binding proteins (GBPs) are soluble dynamin-like proteins that undergo a conformational transition for GTP-controlled oligomerization and disrupt membranes of intracellular parasites to exert their function as part of the innate immune system of mammalian cells. We apply neutron spin echo, X-ray scattering, fluorescence, and EPR spectroscopy as techniques for integrative dynamic structural biology to study the structural basis and mechanism of conformational transitions in the human GBP1 (hGBP1). We mapped hGBP1's essential dynamics from nanoseconds to milliseconds by motional spectra of sub-domains. We find a GTP-independent flexibility of the C-terminal effector domain in the µs-regime and resolve structures of two distinct conformers essential for an opening of hGBP1 like a pocket knife and for oligomerization. Our results on hGBP1's conformational heterogeneity and dynamics (intrinsic flexibility) deepen our molecular understanding relevant for its reversible oligomerization, GTP-triggered association of the GTPase-domains and assembly-dependent GTP-hydrolysis.

Collective dynamics and self-motions in the van der Waals liquid tetrahydrofuran from meso- to inter-molecular scales disentangled by neutron spectroscopy with polarization analysis.

By using time-of-flight neutron spectroscopy with polarization analysis, we have separated coherent and incoherent contributions to the scattering of deuterated tetrahydrofuran in a wide scattering vector (Q)-range from meso- to inter-molecular length scales. The results are compared with those recently reported for water to address the influence of the nature of inter-molecular interactions (van der Waals vs hydrogen bond) on the dynamics. The phenomenology found is qualitatively similar in both systems. Both collective and self-scattering functions are satisfactorily described in terms of a convolution model that considers vibrations, diffusion, and a Q-independent mode. We observe a crossover in the structural relaxation from being dominated by the Q-independent mode at the mesoscale to being dominated by diffusion at inter-molecular length scales. The characteristic time of the Q-independent mode is the same for collective and self-motions and, contrary to water, faster and with a lower activation energy (≈1.4 Kcal/mol) than the structural relaxation time at inter-molecular length scales. This follows the macroscopic viscosity behavior. The collective diffusive time is well described by the de Gennes narrowing relation proposed for simple monoatomic liquids in a wide Q-range entering the intermediate length scales, in contraposition to the case of water.

Nanoscale structure of a hybrid aqueous-nonaqueous electrolyte.

A new class of electrolytes have been reported, hybridizing aqueous with non-aqueous solvents, which combines non-flammability and non-toxicity characteristics of aqueous electrolytes with the superior electrochemical stability of non-aqueous systems. Here, we report measurements of the structure of an electrolyte composed of an equal-mass mixture of 21 m LiTFSI-water and 9 m LiTFSI-dimethyl carbonate using high-energy x-ray diffraction and polarized neutron diffraction with isotope substitution. Neutron structure factors from partially and fully deuterated samples exhibit peaks at low scattering vector Q that we ascribe to long-range correlations involving both solvent molecules and TFSI- anions. We compare both sets of measurements with results of molecular dynamics simulations based on a polarizable force field. The structures derived from simulations are generally in agreement with those measured, except that neutron structure factors predicted for two partially deuterated samples show very intense scattering increasing up to the low-Q limit of simulation, indicating a partial segregation between the two solvents not observed in experimental measurements.

Activated nanoscale actin-binding domain motion in the catenin-cadherin complex revealed by neutron spin echo spectroscopy.

As the core component of the adherens junction in cell-cell adhesion, the cadherin-catenin complex transduces mechanical tension between neighboring cells. Structural studies have shown that the cadherin-catenin complex exists as an ensemble of flexible conformations, with the actin-binding domain (ABD) of α-catenin adopting a variety of configurations. Here, we have determined the nanoscale protein domain dynamics of the cadherin-catenin complex using neutron spin echo spectroscopy (NSE), selective deuteration, and theoretical physics analyses. NSE reveals that, in the cadherin-catenin complex, the motion of the entire ABD becomes activated on nanosecond to submicrosecond timescales. By contrast, in the α-catenin homodimer, only the smaller disordered C-terminal tail of ABD is moving. Molecular dynamics (MD) simulations also show increased mobility of ABD in the cadherin-catenin complex, compared to the α-catenin homodimer. Biased MD simulations further reveal that the applied external forces promote the transition of ABD in the cadherin-catenin complex from an ensemble of diverse conformational states to specific states that resemble the actin-bound structure. The activated motion and an ensemble of flexible configurations of the mechanosensory ABD suggest the formation of an entropic trap in the cadherin-catenin complex, serving as negative allosteric regulation that impedes the complex from binding to actin under zero force. Mechanical tension facilitates the reduction in dynamics and narrows the conformational ensemble of ABD to specific configurations that are well suited to bind F-actin. Our results provide a protein dynamics and entropic explanation for the observed force-sensitive binding behavior of a mechanosensitive protein complex.

Crowding in the Eye Lens: Modeling the Multisubunit Protein ß-Crystallin with a Colloidal Approach.

We present a multiscale characterization of aqueous solutions of the bovine eye lens protein ßH crystallin from dilute conditions up to dynamical arrest, combining dynamic light scattering, small-angle x-ray scattering, tracer-based microrheology, and neutron spin echo spectroscopy. We obtain a comprehensive explanation of the observed experimental signatures from a model of polydisperse hard spheres with additional weak attraction. In particular, the model predictions quantitatively describe the multiscale dynamical results from microscopic nanometer cage diffusion over mesoscopic micrometer gradient diffusion up to macroscopic viscosity. Based on a comparative discussion with results from other crystallin proteins, we suggest an interesting common pathway for dynamical arrest in all crystallin proteins, with potential implications for the understanding of crowding effects in the eye lens.

Enhanced dynamics in the anomalous melting regime of DMPG lipid membranes.

Like many soft materials, lipids undergo a melting transition associated with a significant increase in their dynamics. At temperatures below the main melting transition (Tm ), all molecular and collective dynamics are suppressed, while above Tm the alkyl tail motions, lipid diffusivity, and collective membrane undulations are at least an order of magnitude faster. Here we study the collective dynamics of dimyristoylphosphatidylglycerol (DMPG, di 14:0 PG) using neutron spin echo spectroscopy throughout its anomalous phase transition that occurs over a 12 °C-20° C wide temperature window. Our results reveal that the membranes are softer and more dynamic during the phase transition than at higher temperatures corresponding to the fluid phase and provide direct experimental evidence for the predicted increase in membrane fluctuations during lipid melting. These results provide new insights into the nanoscale lipid membrane dynamics during the melting transition and demonstrate how these dynamics are coupled to changes in the membrane structure.

Resolving Segmental Polymer Dynamics in Nanocomposites by Incoherent Neutron Spin-Echo Spectroscopy.

The segmental dynamics of styrene-butadiene nanocomposites with embedded silica nanoparticles (NPs, ca. 20 vol. %) has been studied by broadband dielectric (BDS) and neutron spin-echo spectroscopy (NSE). It is shown by BDS that overlapping contributions only allow us to conclude on a range of distributions of relaxation times in simplified industrial nanocomposites formed with highly polydisperse NPs. For comparison, structurally similar but less aggregated colloidal nanocomposites have a well-defined distribution of relaxation times due to the reduced influence of interfacial polarization processes. This distribution is widened with respect to the neat polymer, without change in the position of the maximum and at most a small slowing down visible in the average time. We then demonstrate that incoherent NSE can be used to resolve small modifications of segmental dynamics of the industrial samples. By carefully choosing the q-vector of the measurement, experiments with fully hydrogenated polymer give access to the self-dynamics of the polymer in the presence of silica on the scale of approximately 1 nm. Our high-resolution measurements show that the segmental motion is slightly but systematically slowed also by the presence of the industrial filler NPs.

Direct measurement of topological interactions in polymers under shear using neutron spin echo spectroscopy.

We present in-situ neutron spin echo measurements on an entangled polydimethylsiloxane melt under shear and demonstrate the ability to monitor nano-scale dynamics in flowing liquids. We report no changes in the topological interactions of the chains for shear rates approaching the inverse longest relaxation time. Further experiments following along this line will allow to systematically test the predictions of theories, like e.g. convective constraint release.

α-Catenin Structure and Nanoscale Dynamics in Solution and in Complex with F-Actin.

As a core component of the adherens junction, α-catenin stabilizes the cadherin/catenin complexes to the actin cytoskeleton for the mechanical coupling of cell-cell adhesion. α-catenin also modulates actin dynamics, cell polarity, and cell-migration functions that are independent of the adherens junction. We have determined the solution structures of the α-catenin monomer and dimer using in-line size-exclusion chromatography small-angle X-ray scattering, as well as the structure of α-catenin dimer in complex to F-actin filament using selective deuteration and contrast-matching small angle neutron scattering. We further present the first observation, to our knowledge, of the nanoscale dynamics of α-catenin by neutron spin-echo spectroscopy, which explicitly reveals the mobile regions of α-catenin that are crucial for binding to F-actin. In solution, the α-catenin monomer is more expanded than either protomer shown in the crystal structure dimer, with the vinculin-binding M fragment and the actin-binding domain being able to adopt different configurations. The α-catenin dimer in solution is also significantly more expanded than the dimer crystal structure, with fewer interdomain and intersubunit contacts than the crystal structure. When in complex to F-actin, the α-catenin dimer has an even more open and extended conformation than in solution, with the actin-binding domain further separated from the main body of the dimer. The α-catenin-assembled F-actin bundle develops into an ordered filament packing arrangement at increasing α-catenin/F-actin molar ratios. Together, the structural and dynamic studies reveal that α-catenin possesses dynamic molecular conformations that prime this protein to function as a mechanosensor protein.

Dynamics of small unilamellar vesicles.

In this paper, we investigate the dynamics of small unilamellar vesicles with the aid of neutron spin-echo spectroscopy. The purpose of this investigation is twofold. On the one hand, we investigate the influence of solubilised cosurfactant on the dynamics of the vesicle's surfactant bilayer. On the other hand, the small unilamellar vesicles used here have a size between larger vesicles, with dynamics being well described by the Zilman-Granek model and smaller microemulsion droplets which can be described by the Milner-Safran model. Therefore, we want to elucidate the question, which model is more suitable for the description of the membrane dynamics of small vesicles, where the finite curvature of the bilayer is felt by the contained amphiphilic molecules. This question is of substantial relevance for our understanding of membranes and how their dynamics is affected by curvature, a problem that is also of key importance in a number of biological questions. Our results indicate the even down to vesicle radii of 20 nm the Zilman-Granek model appears to be the more suitable one.

Temperature-dependent structure and dynamics of highly-branched poly(N-isopropylacrylamide) in aqueous solution.

Small-angle neutron scattering (SANS) and neutron spin-echo (NSE) have been used to investigate the temperature-dependent solution behaviour of highly-branched poly(N-isopropylacrylamide) (HB-PNIPAM). SANS experiments have shown that water is a good solvent for both HB-PNIPAM and a linear PNIPAM control at low temperatures where the small angle scattering is described by a single correlation length model. Increasing the temperature leads to a gradual collapse of HB-PNIPAM until above the lower critical solution temperature (LCST), at which point aggregation occurs, forming disperse spherical particles of up to 60 nm in diameter, independent of the degree of branching. However, SANS from linear PNIPAM above the LCST is described by a model that combines particulate structure and a contribution from solvated chains. NSE was used to study the internal and translational solution dynamics of HB-PNIPAM chains below the LCST. Internal HB-PNIPAM dynamics is described well by the Rouse model for non-entangled chains.

Dramatic influence of patchy attractions on short-time protein diffusion under crowded conditions.

In the dense and crowded environment of the cell cytoplasm, an individual protein feels the presence of and interacts with all surrounding proteins. While we expect this to strongly influence the short-time diffusion coefficient Ds of proteins on length scales comparable to the nearest-neighbor distance, this quantity is difficult to assess experimentally. We demonstrate that quantitative information about Ds can be obtained from quasi-elastic neutron scattering experiments using the neutron spin echo technique. We choose two well-characterized and highly stable eye lens proteins, bovine α-crystallin and γB-crystallin, and measure their diffusion at concentrations comparable to those present in the eye lens. While diffusion slows down with increasing concentration for both proteins, we find marked variations that are directly linked to subtle differences in their interaction potentials. A comparison with computer simulations shows that anisotropic and patchy interactions play an essential role in determining the local short-time dynamics. Hence, our study clearly demonstrates the enormous effect that weak attractions can have on the short-time diffusion of proteins at concentrations comparable to those in the cellular cytosol.

Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding.

BACKGROUND: Human lactoferrin is an iron-binding protein of the innate immune system consisting of two connected lobes, each with a binding site located in a cleft. The clefts in each lobe undergo a hinge movement from open to close when Fe3+ is present in the solution and can be bound. The binding mechanism was assumed to relate on thermal domain fluctuations of the cleft domains prior to binding. We used Small Angle Neutron Scattering and Neutron Spin Echo Spectroscopy to determine the lactoferrin structure and domain dynamics in solution. RESULTS: When Fe3+ is present in solution interparticle interactions change from repulsive to attractive in conjunction with emerging metas aggregates, which are not observed without Fe3+. The protein form factor shows the expected change due to lobe closing if Fe3+ is present. The dominating motions of internal domain dynamics with relaxation times in the 30-50 ns range show strong bending and stretching modes with a steric suppressed torsion, but are almost independent of the cleft conformation. Thermally driven cleft closing motions of relevant amplitude are not observed if the cleft is open. CONCLUSION: The Fe3+ binding mechanism is not related to thermal equilibrium fluctuations closing the cleft. A likely explanation may be that upon entering the cleft the iron ion first binds weakly which destabilizes and softens the hinge region and enables large fluctuations that then close the cleft resulting in the final formation of the stable iron binding site and, at the same time, stable closed conformation.

Structure and dynamics of polyelectrolyte surfactant mixtures under conditions of surfactant excess.

Oppositely charged polyelectrolyte (PE) surfactant mixtures can self-assemble into a large variety of mesoscopic structures, so-called polyelectrolyte surfactant complexes (PESCs). These structures directly affect the macroscopic behavior of such solutions. In this study, we investigated mixtures of the cationically charged PE JR 400 and the anionic surfactant SDS with the help of different neutron scattering and fluorescence methods. While an excess of PE charges in semi-dilute solutions causes an increase of viscosity, it has been observed that an excess of surfactant charges reduces the viscosity while precipitation is observed at charge equilibrium. The increase in viscosity had been investigated before and was attributed to the formation of cross links between PE chains. In this publication we focus our attention on the reduction of viscosity which is observed with an excess of surfactant charges. It is found that the PE chains form relatively large and densely packed clusters near the phase boundary on the surfactant rich side, thereby occupying less space and reducing the viscosity. For even higher surfactant concentrations, individual surfactant decorated PE chains are observed and their viscosity is found to be similar to that of the pure PE.

Unusual dynamics of concentration fluctuations in solutions of weakly attractive globular proteins.

The globular protein γB-crystallin exhibits a complex phase behavior, where liquid-liquid phase separation characterized by a critical volume fraction ϕc = 0.154 and a critical temperature Tc = 291.8 K coexists with dynamical arrest on all length scales at volume fractions around ϕ ≈ 0.3-0.35, and an arrest line that extends well into the unstable region below the spinodal. However, although the static properties such as the osmotic compressibility and the static correlation length are in quantitative agreement with predictions for binary liquid mixtures, this is not the case for the dynamics of concentration fluctuations described by the dynamic structure factor S(q,t). Using a combination of dynamic light scattering and neutron spin echo measurements, we demonstrate that the competition between critical slowing down and dynamical arrest results in a much more complex wave vector dependence of S(q,t) than previously anticipated.

On the mesoscopic origins of high viscosities in some polyelectrolyte-surfactant mixtures.

Oppositely charged polyelectrolyte (PE) surfactant mixtures allow the control of rheological parameters of a solution even at fairly low concentrations. For example, addition of 0.3 wt. % of anionic surfactant to a 1 wt. % solution of the polycation JR 400 increases the viscosity by 4 orders of magnitude. Recently, we could show that this increase is related to the formation of mixed, rod-like PE/surfactant aggregates which interconnect several polyelectrolyte chains [Hoffmann et al., Europhys. Lett. 104, 28001 (2013)]. In this paper, we refine our structural model of the aggregates to obtain a more consistent picture of their internal structure for different anionic surfactants. Combining small angle neutron scattering (SANS) and neutron spin-echo (NSE) allows us to determine the size of the aggregates. By comparing different contrasts, the internal structure of the aggregates can be elucidated and it is seen that the PE in the aggregates retains a relatively high freedom of movement. We proceeded to investigate the influence of the surfactant concentration and the surfactant type on structure and dynamics of the mixed aggregates. It is seen that the structural parameters of the aggregates depend very little on the surfactant concentration and headgroup. However, it is crucial to incorporate a sufficient amount of PE in the aggregates to increase the viscosity of the aggregates. By comparing viscous samples at 1 wt. % PE concentration with samples at a PE concentration of 0.3 wt. %, where no significant increase in viscosity is observed, we find that similar aggregates are formed already at this lower PE concentrations. However, the amount of PE incorporated in them is insufficient to interconnect several PE chains and therefore, they do not increase viscosity. So, our detailed investigation combining contrast variation SANS and NSE does not only allow to explain the viscosity behavior but also to deduced detailed information regarding the structures and the dynamics especially of the polyelectrolyte within the complexes.

Structural and microscopic relaxations in a colloidal glass.

The aging dynamics of a colloidal glass has been studied by multiangle dynamic light scattering, neutron spin echo, X-ray photon correlation spectroscopy and molecular dynamics simulations. The two relaxation processes, microscopic (fast) and structural (slow), have been investigated in an unprecedentedly wide range of time and length scales covering both ergodic and nonergodic regimes. The microscopic relaxation time remains diffusive at all length scales across the glass transition scaling with wavevector Q as Q(-2). The length-scale dependence of structural relaxation time changes from diffusive, characterized by a Q(-2)-dependence in the early stages of aging, to a Q(-1)-dependence in the full aging regime which marks a discontinuous hopping dynamics. Both regimes are associated with a stretched behaviour of the correlation functions. We expect these findings to provide a general description of both relaxations across the glass transition.

Bilayer undulation dynamics in unilamellar phospholipid vesicles: effect of temperature, cholesterol and trehalose.

We report a combined dynamic light scattering (DLS) and neutron spin-echo (NSE) study on the local bilayer undulation dynamics of phospholipid vesicles composed of 1,2-dimyristoyl-glycero-3-phosphatidylcholine (DMPC) under the influence of temperature and the additives cholesterol and trehalose. The additives affect vesicle size and self-diffusion. Mechanical properties of the membrane and corresponding bilayer undulations are tuned by changing lipid headgroup or acyl chain properties through temperature or composition. On the local length scale, changes at the lipid headgroup influence the bilayer bending rigidity κ less than changes at the lipid acyl chain: We observe a bilayer softening around the main phase transition temperature Tm of the single lipid system, and stiffening when more cholesterol is added, in concordance with literature. Surprisingly, no effect on the mechanical properties of the vesicles is observed upon the addition of trehalose.

Softening of phospholipid membranes by the adhesion of silica nanoparticles--as seen by neutron spin-echo (NSE).

The interactions between nanoparticles and vesicles are of significant interest both from a fundamental as well as from a practical point of view, as vesicles can serve as a model system for cell membranes. Accordingly the effect of nanoparticles that bind to the vesicle bilayer is very important with respect to understanding their biological impact and also may shed some light on the mechanisms behind the effect of nanotoxicity. In this study we have investigated the influence of small adsorbed silica nanoparticles (SiNPs) on the structure of zwitterionic DOPC vesicles. By a combination of SANS, cryo-TEM, and DLS, we observed that the SiNPs are bound to the outer vesicle surface without significantly affecting the vesicle structure. Most interestingly, by means of neutron spin-echo (NSE) local bilayer fluctuations were studied and one finds a small but marked decrease of the membrane rigidity upon binding of the nanoparticles. This surprising finding may be a relevant aspect for the further understanding of the effects that nanoparticles have on phospholipid bilayers.

Compact structure and non-Gaussian dynamics of ring polymer melts.

We present a neutron scattering analysis of the structure and dynamics of PEO polymer rings with a molecular weight 2.5 times higher than the entanglement mass. The melt structure was found to be more compact than a Gaussian model would suggest. With increasing time the center of mass (c.o.m.) diffusion undergoes a transition from sub-diffusive to diffusive behavior. The transition time agrees well with the decorrelation time predicted by a mode coupling approach. As a novel feature well pronounced non-Gaussian behavior of the c.o.m. diffusion was found that shows surprising analogies to the cage effect known from glassy systems. Finally, the longest wavelength Rouse modes are suppressed possibly as a consequence of an onset of lattice animal features as hypothesized in theoretical approaches.