Dynamic Implications of Noncovalent Interactions in Amphiphilic Single-Chain Polymer Nanoparticles.

Single-chain polymer nanoparticles (SCNPs) combine the chemical diversity of synthetic polymers with the intricate structure of biopolymers, generating versatile biomimetic materials. The mobility of polymer chain segments at length scales similar to secondary structural elements in proteins is critical to SCNP structure and thus function. However, the influence of noncovalent interactions used to form SCNPs (e.g., hydrogen-bonding and biomimetic secondary-like structure) on these conformational dynamics is challenging to quantitatively assess. To isolate the effects of noncovalent interactions on SCNP structure and conformational dynamics, we synthesized a series of amphiphilic copolymers containing dimethylacrylamide and monomers capable of forming these different interactions: (1) di(phenylalanine) acrylamide that forms intramolecular ß-sheet-like cross-links, (2) phenylalanine acrylamide that forms hydrogen-bonds but lacks a defined local structure, and (3) benzyl acrylamide that has the lowest propensity for hydrogen-bonding. Each SCNP formed folded structures comparable to those of intrinsically disordered proteins, as observed by size exclusion chromatography and small angle neutron scattering. The dynamics of these polymers, as characterized by a combination of dynamic light scattering and neutron spin echo spectroscopy, was well described using the Zimm with internal friction (ZIF) model, highlighting the role of each noncovalent interaction to additively restrict the internal relaxations of SCNPs. These results demonstrate the utility of local scale interactions to control SCNP polymer dynamics, guiding the design of functional biomimetic materials with refined binding sites and tunable kinetics.

Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations.

Cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.

From ionic clusters dynamics to network constraints in ionic polymer solutions.

Physical networks formed by ionizable polymers with ionic clusters as crosslinks are controlled by coupled dynamics that transcend from ionic clusters through chain motion to macroscopic response. Here, the coupled dynamics, across length scales, from the ionic clusters to the networks in toluene swollen polystyrene sulfonate networks, were directly correlated, as the electrostatic environment of the physical crosslinks was altered. The multiscale insight is attained by coupling neutron spin echo measurements with molecular dynamics simulations, carried out to times typical of relaxation of polymers in solutions. The experimental dynamic structure factor is in outstanding agreement with the one calculated from computer simulations, as the networks are perturbed by elevating the temperature and changing the electrostatic environment. In toluene, the long-lived clusters remain stable over hundreds of ns across a broad temperature range, while the polymer network remains dynamic. Though the size of the clusters changes as the dielectric constant of the solvent is modified through the addition of ethanol, they remain stable but morph, enhancing the polymer chain dynamics.

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy.

Most human body proteins' activity and functionality are related to configurational changes of entire subdomains within the protein crystal structure. The crystal structures build the basis for any calculation that describes the structure or dynamics of a protein, most of the time with strong geometrical restrictions. However, these restrictions from the crystal structure are not present in the solution. The structure of the proteins in the solution may differ from the crystal due to rearrangements of loops or subdomains on the pico to nanosecond time scale (i.e., the internal protein dynamics time regime). The present work describes how slow motions on timescales of several tens of nanoseconds can be accessed using neutron scattering. In particular, the dynamical characterization of two major human proteins, an intrinsically disordered protein that lacks a well-defined secondary structure and a classical antibody protein, is addressed by neutron spin echo spectroscopy (NSE) combined with a wide range of laboratory characterization methods. Further insights into protein domain dynamics were achieved using mathematical modeling to describe the experimental neutron data and determine the crossover between combined diffusive and internal protein motions. The extraction of the internal dynamic contribution to the intermediate scattering function obtained from NSE, including the timescale of the various movements, allows further vision into the mechanical properties of single proteins and the softness of proteins in their nearly natural environment in the crowded protein solution.

Acetaminophen Interactions with Phospholipid Vesicles Induced Changes in Morphology and Lipid Dynamics.

Acetaminophen (APAP) or paracetamol, despite its wide and common use for pain and fever symptoms, shows a variety of side effects, toxic effects, and overdose effects. The most common form of toxic effects of APAP is in the liver where phosphatidylcholine is the major component of the cell membrane with additional associated functionalities. Although this is the case, the effects of APAP on pure phospholipid membranes have been largely ignored. Here, we used 1,2-di-(octadecenoyl)-sn-glycero-3-phosphocholine (DOPC), a commonly found phospholipid in mammalian cell membranes, to synthesize large unilamellar vesicles to investigate how the incorporation of APAP changes the pure lipid vesicle structure, morphology, and fluidity at different concentrations. We used a combination of dynamic light scattering, small-angle neutron and X-ray scattering (SANS, SAXS), and cryo-TEM for structural characterization, and neutron spin-echo (NSE) spectroscopy to investigate the dynamics. We showed that the incorporation of APAP in the lipid bilayer significantly impacts the spherical phospholipid self-assembly in terms of its morphology and influences the lipid content in the bilayer, causing a decrease in bending rigidity. We observe a decrease in the number of lipids per vesicle by almost 28% (0.06 wt % APAP) and 19% (0.12 wt % APAP) compared to the pure DOPC (0 wt % APAP). Our results showed that the incorporation of APAP reduces the membrane rigidity by almost 50% and changes the spherical unilamellar vesicles into much more irregularly shaped vesicles. Although the bilayer structure did not show much change when observed by SAXS, NSE and cryo-TEM results showed the lipid dynamics change with the addition of APAP in the bilayer, which causes the overall decreased membrane rigidity. A strong effect on the lipid tail motion showed that the space explored by the lipid tails increases by a factor of 1.45 (for 0.06 wt % APAP) and 1.75 (for 0.12 wt % APAP) compared to DOPC without the drug.

Magnetic charge's relaxation propelled electricity in two-dimensional magnetic honeycomb lattice.

Emerging new concepts, such as magnetic charge dynamics in two-dimensional magnetic material, can provide novel mechanism for spin-based electrical transport at macroscopic length. In artificial spin ice of single domain elements, magnetic charge's relaxation can create an efficient electrical pathway for conduction by generating fluctuations in local magnetic field that couple with conduction electron spins. In a first demonstration, we show that the electrical conductivity is propelled by more than an order of magnitude at room temperature due to magnetic charge defects sub-picosecond relaxation in artificial magnetic honeycomb lattice. The direct evidence to the proposed electrical conduction mechanism in two-dimensional frustrated magnet points to the untapped potential for spintronic applications in this system.

Manipulating Phospholipid Vesicles at the Nanoscale: A Transformation from Unilamellar to Multilamellar by an n-Alkyl-poly(ethylene oxide).

We investigated the influence of an n-alkyl-PEO polymer on the structure and dynamics of phospholipid vesicles. Multilayer formation and about a 9% increase in the size in vesicles were observed by cryogenic transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), and small-angle neutron/X-ray scattering (SANS/SAXS). The results indicate a change in the lamellar structure of the vesicles by a partial disruption caused by polymer chains, which seems to correlate with about a 30% reduction in bending rigidity per unit bilayer, as revealed by neutron spin echo (NSE) spectroscopy. Also, a strong change in lipid tail relaxation was observed. Our results point to opportunities using synthetic polymers to control the structure and dynamics of membranes, with possible applications in technical materials and also in drug and nutraceutical delivery.

Membrane stiffness and myelin basic protein binding strength as molecular origin of multiple sclerosis.

Myelin basic protein (MBP) and its interaction with lipids of the myelin sheath plays an important part in the pathology of multiple sclerosis (MS). Previous studies observed that changes in the myelin lipid composition lead to instabilities and enhanced local curvature of MBP-lipid multilayer structures. We investigated the molecular origin of the instability and found that the diseased lipid membrane has a 25% lower bending rigidity, thus destabilizing smooth [Formula: see text]µm curvature radius structures such as in giant unilamellar vesicles. MBP-mediated assembling of lipid bilayers proceeds in two steps, with a slow second step occurring over many days where native lipid membranes assemble into well-defined multilayer structures, whereas diseased lipid membranes form folded assemblies with high local curvature. For both native and diseased lipid mixtures we find that MBP forms dense liquid phases on top of the lipid membranes mediating attractive membrane interactions. Furthermore, we observe MBP to insert into its bilayer leaflet side in case of the diseased lipid mixture, whereas there is no insertion for the native mixture. Insertion increases the local membrane curvature, and could be caused by a decrease of the sphingomyelin content of the diseased lipid mixture. These findings can help to open a pathway to remyelination strategies.

How cholesterol stiffens unsaturated lipid membranes.

Cholesterol is an integral component of eukaryotic cell membranes and a key molecule in controlling membrane fluidity, organization, and other physicochemical parameters. It also plays a regulatory function in antibiotic drug resistance and the immune response of cells against viruses, by stabilizing the membrane against structural damage. While it is well understood that, structurally, cholesterol exhibits a densification effect on fluid lipid membranes, its effects on membrane bending rigidity are assumed to be nonuniversal; i.e., cholesterol stiffens saturated lipid membranes, but has no stiffening effect on membranes populated by unsaturated lipids, such as 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). This observation presents a clear challenge to structure-property relationships and to our understanding of cholesterol-mediated biological functions. Here, using a comprehensive approach-combining neutron spin-echo (NSE) spectroscopy, solid-state deuterium NMR (2H NMR) spectroscopy, and molecular dynamics (MD) simulations-we report that cholesterol locally increases the bending rigidity of DOPC membranes, similar to saturated membranes, by increasing the bilayer's packing density. All three techniques, inherently sensitive to mesoscale bending fluctuations, show up to a threefold increase in effective bending rigidity with increasing cholesterol content approaching a mole fraction of 50%. Our observations are in good agreement with the known effects of cholesterol on the area-compressibility modulus and membrane structure, reaffirming membrane structure-property relationships. The current findings point to a scale-dependent manifestation of membrane properties, highlighting the need to reassess cholesterol's role in controlling membrane bending rigidity over mesoscopic length and time scales of important biological functions, such as viral budding and lipid-protein interactions.

Uncoupling between the lipid membrane dynamics of differing hierarchical levels.

Diverse biological functions of biomembranes are made possible by their rich dynamic behaviors across multiple scales. While the potential coupling between the dynamics of differing scales may underlie the machineries regulating the biomembrane-involving processes, the mechanism and even the existence of this coupling remain an open question, despite the latter being taken for granted. Via inelastic neutron scattering, we examined dynamics across multiple scales for the lipid membranes whose dynamic behaviors were perturbed by configurational changes at two membrane regions. Surprisingly, the dynamic behavior of individual lipid molecules and their collective motions were not always coupled. This suggests that the expected causal relation between the dynamics of the differing hierarchical levels does not exist and that an apparent coupling can emerge by manipulating certain membrane configurations. The findings provide insight on biomembrane modeling and how cells might individually or concertedly control the multiscale membrane dynamics to regulate their functions.

Reduced Internal Friction by Osmolyte Interaction in Intrinsically Disordered Myelin Basic Protein.

Urea is a strong denaturing osmolyte that disrupts noncovalent bonds in proteins. Here, we present a small-angle neutron scattering (SANS) and neutron spin-echo spectroscopy (NSE) study on the structure and dynamics of the intrinsically disordered myelin basic protein (MBP) denatured by urea. SANS results show that urea-denatured MBP is more compact than ideal polymers, while its secondary structure content is entirely lost. NSE experiments reveal concomitantly an increase of the relaxation time and of the amplitude of internal motions in urea-denatured MBP as compared to native MBP. If interpreted in terms of the Zimm model including internal friction (ZIF), the internal friction parameter decreased by a factor of 6.5. Urea seems to not only smooth local energy barriers, reducing internal friction on a local scale, but also significantly reduces the overall depth of the global energy landscape. This leads to a nearly complete loss of restoring forces beyond entropic forces and in turn allows for larger motional amplitudes. Obviously, the noncovalent H-bonds are largely eliminated, driving the unfolded protein to be more similar to a synthetic polymer.

Influence of Chemically Disrupted Photosynthesis on Cyanobacterial Thylakoid Dynamics in Synechocystis sp. PCC 6803.

The photosynthetic machinery of the cyanobacterium Synechocystis sp. PCC 6803 resides in flattened membrane sheets called thylakoids, situated in the peripheral part of the cellular cytoplasm. Under photosynthetic conditions these thylakoid membranes undergo various dynamical processes that could be coupled to their energetic functions. Using Neutron Spin Echo Spectroscopy (NSE), we have investigated the undulation dynamics of Synechocystis sp. PCC 6803 thylakoids under normal photosynthetic conditions and under chemical treatment with DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea), an herbicide that disrupts photosynthetic electron transfer. Our measurements show that DCMU treatment has a similar effect as dark conditions, with differences in the undulation modes of the untreated cells compared to the chemically inhibited cells. We found that the disrupted membranes are 1.5-fold more rigid than the native membranes during the dark cycle, while in light they relax approximately 1.7-fold faster than native and they are 1.87-fold more flexible. The strength of the herbicide disruption effect is characterized further by the damping frequency of the relaxation mode and the decay rate of the local shape fluctuations. In the dark, local thicknesses and shape fluctuations relax twice as fast in native membranes, at 17% smaller mode amplitude, while in light the decay rate of local fluctuations is 1.2-fold faster in inhibited membranes than in native membranes, at 56% higher amplitude. The disrupted electron transfer chain and the decreased proton motive force within the lumenal space partially explain the variations observed in the mechanical properties of the Synechocystis membranes, and further support the hypothesis that the photosynthetic process is tied to thylakoid rigidity in this type of cyanobacterial cell.

A comparison of the network structure and inner dynamics of homogeneously and heterogeneously crosslinked PNIPAM microgels with high crosslinker content.

Poly(N-isopropylacrylamide) microgel particles were prepared via a "classical" surfactant-free precipitation polymerization and a continuous monomer feeding approach. It is anticipated that this yields microgel particles with different internal structures, namely a dense core with a fluffy shell for the classical approach and a more even crosslink distribution in the case of the continuous monomer feeding approach. A thorough structural investigation of the resulting microgels with dynamic light scattering, atomic force microscopy and small angle neutron scattering was conducted and related to neutron spin echo spectroscopy data. In this way a link between structural and dynamic features of the internal polymer network was made.

Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells.

Translational diffusion of macromolecules in cell is generally assumed to be anomalous due high macromolecular crowding of the milieu. Red blood cells are a special case of cells filled quasi exclusively (95% of the dry weight of the cell) with an almost spherical protein: hemoglobin. Hemoglobin diffusion has since a long time been recognized as facilitating the rate of oxygen diffusion through a solution. We address in this paper the question on how hemoglobin diffusion in the red blood cells can help the oxygen capture at the cell level and hence to improve oxygen transport. We report a measurement by neutron spin echo spectroscopy of the diffusion of hemoglobin in solutions with increasing protein concentration. We show that hemoglobin diffusion in solution can be described as Brownian motion up to physiological concentration and that hemoglobin diffusion in the red blood cells and in solutions at similar concentration are the same. Finally, using a simple model and the concentration dependence of the diffusion of the protein reported here, we show that hemoglobin concentration observed in human red blood cells ([Formula: see text]330 g.L -1) corresponds to an optimum for oxygen transport for individuals under strong activity.

Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics.

The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The "tip of the whip" that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the binding of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.

Fast antibody fragment motion: flexible linkers act as entropic spring.

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.

Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells.

Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

Internal nanosecond dynamics in the intrinsically disordered myelin basic protein.

Intrinsically disordered proteins lack a well-defined folded structure and contain a high degree of structural freedom and conformational flexibility, which is expected to enhance binding to their physiological targets. In solution and in the lipid-free state, myelin basic protein belongs to that class of proteins. Using small-angle scattering, the protein was found to be structurally disordered similar to Gaussian chains. The combination of structural and hydrodynamic information revealed an intermediary compactness of the protein between globular proteins and random coil polymers. Modeling by a coarse-grained structural ensemble gave indications for a compact core with flexible ends. Neutron spin-echo spectroscopy measurements revealed a large contribution of internal dynamics to the overall diffusion. The experimental results showed a high flexibility of the structural ensemble. Displacement patterns along the first two normal modes demonstrated that collective stretching and bending motions dominate the internal modes. The observed dynamics represent nanosecond conformational fluctuations within the reconstructed coarse-grained structural ensemble, allowing the exploration of a large configurational space. In an alternative approach, we investigated if models from polymer theory, recently used for the interpretation of fluorescence spectroscopy experiments on disordered proteins, are suitable for the interpretation of the observed motions. Within the framework of the Zimm model with internal friction (ZIF), a large offset of 81.6 ns is needed as an addition to all relaxation times due to intrachain friction sources. The ZIF model, however, shows small but systematic deviations from the measured data. The large value of the internal friction leads to the breakdown of the Zimm model.