Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments.

This study investigates possible structural changes of an intrinsically disordered protein (IDP) when it adsorbs to a solid surface. Experiments on IDPs primarily result in ensemble averages due to their high dynamics. Therefore, molecular dynamics (MD) simulations are crucial for obtaining more detailed information on the atomistic and molecular levels. An evaluation of seven different force field and water model combinations have been applied: (A) CHARMM36IDPSFF + CHARMM-modified TIP3P, (B) CHARMM36IDPSFF + TIP4P-D, (C) CHARMM36m + CHARMM-modified TIP3P, (D) AMBER99SB-ILDN + TIP3P, (E) AMBER99SB-ILDN + TIP4P-D, (F) AMBERff03ws + TIP4P/2005, and (G) AMBER99SB-disp + disp-water. The results have been qualitatively compared with those of small-angle X-ray scattering, synchrotron radiation circular dichroism spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The model IDP corresponds to the first 33 amino acids of the N-terminal of the magnesium transporter A (MgtA) and is denoted as KEIF. With a net charge of +3, KEIF is found to adsorb to the anionic synthetic clay mineral Laponite® due to the increase in entropy from the concomitant release of counterions from the surface. The experimental results show that the peptide is largely disordered with a random coil conformation, whereas the helical content (α- and/or 310-helices) increased upon adsorption. MD simulations corroborate these findings and further reveal an increase in polyproline II helices and an extension of the peptide conformation in the adsorbed state. In addition, the simulations provided atomistic resolution of the adsorbed ensemble of structures, where the arginine residues had a high propensity to form hydrogen bonds with the surface. Simulations B, E, and G showed significantly better agreement with experiments than the other simulations. Particularly noteworthy is the discovery that B and E with TIP4P-D water had superior performance to their corresponding simulations A and D with TIP3P-type water. Thus, this study shows the importance of the water model when simulating IDPs and has also provided an insight into the structural changes of surface-active IDPs induced by adsorption, which may play an important role in their function.

The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions.

Intrinsically disordered proteins (IDP) are proteins that sample a heterogeneous ensemble of conformers in solution. An estimated 25-30% of all eukaryotic proteins belong to this class. In vivo, IDPs function under conditions that are highly crowded by other biological macromolecules. Previous research has highlighted that the presence of crowding agents can influence the conformational ensemble sampled by IDPs, resulting in either compaction or expansion. The effects of self-crowding of the disordered protein Histatin 5 has, in an earlier study, been found to have limited influence on the conformational ensemble. In this study, it is examined whether the short chain length of Histatin 5 can explain the limited effects of crowding observed, by introducing (Histatin 5)2, a tandem repeat of Histatin 5. By utilizing small-angle X-ray scattering, it is shown that the conformational ensemble is conserved at high protein concentrations, in resemblance with Histatin 5, although with a lowered protein concentration at which aggregation arises. Under dilute conditions, atomistic molecular dynamics and coarse-grained Monte Carlo simulations, as well as an established scaling law, predicted more extended conformations than indicated by experimental data, hence implying that (Histatin 5)2 does not behave as a self-avoiding random walk.

Supracolloidal Atomium.

Nature suggests that complex materials result from a hierarchical organization of matter at different length scales. At the nano- and micrometer scale, macromolecules and supramolecular aggregates spontaneously assemble into supracolloidal structures whose complexity is given by the coexistence of various colloidal entities and the specific interactions between them. Here, we demonstrate how such control can be implemented by engineering specially customized bile salt derivative-based supramolecular tubules that exhibit a highly specific interaction with polymeric microgel spheres at their extremities thanks to their scroll-like structure. This design allows for hierarchical supracolloidal self-assembly of microgels and supramolecular scrolls into a regular framework of "nodes" and "linkers". The supramolecular assembly into scrolls can be triggered by pH and temperature, thereby providing the whole supracolloidal system with interesting stimuli-responsive properties. A colloidal smart assembly is embodied with features of center-linker frameworks as those found in molecular metal-organic frameworks and in structures engineered at human scale, masterfully represented by the Atomium in Bruxelles.

Physicochemical Characterisation of KEIF-The Intrinsically Disordered N-Terminal Region of Magnesium Transporter A.

Magnesium transporter A (MgtA) is an active transporter responsible for importing magnesium ions into the cytoplasm of prokaryotic cells. This study focuses on the peptide corresponding to the intrinsically disordered N-terminal region of MgtA, referred to as KEIF. Primary-structure and bioinformatic analyses were performed, followed by studies of the undisturbed single chain using a combination of techniques including small-angle X-ray scattering, circular dichroism spectroscopy, and atomistic molecular-dynamics simulations. Moreover, interactions with large unilamellar vesicles were investigated by using dynamic light scattering, laser Doppler velocimetry, cryogenic transmission electron microscopy, and circular dichroism spectroscopy. KEIF was confirmed to be intrinsically disordered in aqueous solution, although extended and containing little ß -structure and possibly PPII structure. An increase of helical content was observed in organic solvent, and a similar effect was also seen in aqueous solution containing anionic vesicles. Interactions of cationic KEIF with anionic vesicles led to the hypothesis that KEIF adsorbs to the vesicle surface through electrostatic and entropic driving forces. Considering this, there is a possibility that the biological role of KEIF is to anchor MgtA in the cell membrane, although further investigation is needed to confirm this hypothesis.

A microgel-Pickering emulsion route to colloidal molecules with temperature-tunable interaction sites.

A simple Pickering emulsion route has been developed for the assembly of temperature-responsive poly(N-isopropylacrylamide) (PNIPAM) microgel particles into colloidal molecules comprising a small number of discrete microgel interaction sites on a central oil emulsion droplet. Here, the surface activity of the microgels serves to drive their assembly through adsorption to growing polydimethylsiloxane (PDMS) emulsion oil droplets of high monodispersity, prepared in situ via ammonia-catalysed hydrolysis and condensation of dimethyldiethoxysilane (DMDES). A dialysis step is employed in order to limit further growth once the target assembly size has been reached, thus yielding narrowly size-distributed, colloidal molecule-like microgel-Pickering emulsion oil droplets with well-defined microgel interaction sites. The temperature-responsiveness of the PNIPAM interaction sites will allow for the directional interactions to be tuned in a facile manner with temperature, all the way from soft repulsive to short-range attractive as the their volume phase transition temperature (VPTT) is crossed. Finally, the microgel-Pickering emulsion approach is extended to a mixture of PNIPAM and poly(N-isopropylmethacrylamide) (PNIPMAM) microgels that differ with respect to their VPTT, this in order to prepare patchy colloidal molecules where the directional interactions will be more readily resolved.

Preparation of colloidal molecules with temperature-tunable interactions from oppositely charged microgel spheres.

The self-assembly of small colloidal clusters, so-called colloidal molecules, into crystalline materials has proven extremely challenging, the outcome often being glassy, amorphous states where positions and orientations are locked. In this paper, a new type of colloidal molecule is therefore prepared, assembled from poly(N-isopropylacrylamide) (PNIPAM)-based microgels that due to their well documented softness and temperature-response allow for greater defect tolerance compared to hard spheres and for convenient in situ tuning of size, volume fraction and inter-particle interactions with temperature. The microgels (B) are assembled by electrostatic adsorption onto oppositely charged, smaller-sized microgels (A), where the relative size of the two determines the valency (n) of the resulting core-satellite ABn-type colloidal molecules. Following assembly, a microfluidic deterministic lateral displacement (DLD) device is used to effectively isolate AB4-type colloidal molecules of tetrahedral geometry that possess a repulsive-to-attractive transition on crossing the microgels' volume phase transition temperature (VPTT). These soft, temperature-responsive colloidal molecules constitute highly promising building blocks for the preparation of new materials with emergent properties, and their optical wavelength-size makes them especially interesting for optical applications.

A Droplet-Based Microfluidics Route to Temperature-Responsive Colloidal Molecules.

Small clusters of spherical colloids that mimic real molecules, so-called colloidal molecules, hold great promise as building blocks in bottom-up routes to new materials. However, their typical hard sphere nature has hampered their assembly into ordered structures, largely due to a lack of control in the interparticle interactions. To provide easy external control of the interactions, the present work focuses on the preparation of colloidal molecules from temperature-responsive microgel particles that undergo a transition from a soft repulsive to a short-range attractive state as their characteristic volume phase transition temperature (VPTT) is crossed. Preparation of the colloidal molecules starts with the use of a droplet-based microfluidics device to form highly uniform water-in-oil (W/O) emulsion droplets containing, on average and with a narrow distribution, four microgels per droplet. Evaporation of the water then leads to the formation of colloidal molecule-like clusters, which can be harvested following cross-linking and phase transfer. We use a mixture of two types of microgels, one based on poly(N-isopropylacrylamide) (PNIPAM) and the other on poly(N-isopropylmethacrylamide) (PNIPMAM), to prepare bicomponent colloidal molecules, and show that the difference in VPTT between the two allows for induction of attractive interparticle interactions between the PNIPAM interaction sites at temperatures in between the two VPTTs, analogous to the interactions among patchy biomacromolecules such as many proteins.

Assembling responsive microgels at responsive lipid membranes.

Directed colloidal self-assembly at fluid interfaces can have a large impact in the fields of nanotechnology, materials, and biomedical sciences. The ability to control interfacial self-assembly relies on the fine interplay between bulk and surface interactions. Here, we investigate the interfacial assembly of thermoresponsive microgels and lipogels at the surface of giant unilamellar vesicles (GUVs) consisting of phospholipids bilayers with different compositions. By altering the properties of the lipid membrane and the microgel particles, it is possible to control the adsorption/desorption processes as well as the organization and dynamics of the colloids at the vesicle surface. No translocation of the microgels and lipogels through the membrane was observed for any of the membrane compositions and temperatures investigated. The lipid membranes with fluid chains provide highly dynamic interfaces that can host and mediate long-range ordering into 2D hexagonal crystals. This is in clear contrast to the conditions when the membranes are composed of lipids with solid chains, where there is no crystalline arrangement, and most of the particles desorb from the membrane. Likewise, we show that in segregated membranes, the soft microgel colloids form closely packed 2D crystals on the fluid bilayer domains, while hardly any particles adhere to the more solid bilayer domains. These findings thus present an approach for selective and controlled colloidal assembly at lipid membranes, opening routes toward the development of tunable soft materials.

Anisotropic responsive microgels with tuneable shape and interactions.

Highly monodisperse polystyrene/poly(N-isopropylmethacrylamide) (PS-PNIPMAM) core-shell composite microgels were synthesized and further nanoengineered in either ellipsoidal, faceted or bowl-shaped particles. Beside their anisotropy in shape, the microgel design enables an exquisite control of the particle conformation, size and interactions from swollen and hydrophilic to collapsed and hydrophobic using temperature as an external control variable. The post-processing procedures and the characterization of the different particles are first presented. Their potential as model systems for the investigation of the effects of anisotropic shape and interactions on the phase behavior is further demonstrated. Finally, the self-assembly of bowl-shaped composite microgel particles is discussed, where the temperature and an external AC electric field are employed to control the interactions from repulsive to attractive and from soft repulsive to dipolar, respectively.

A new route towards colloidal molecules with externally tunable interaction sites.

We describe a route towards self-assembled colloidal molecules, where thermoresponsive microgels serve as discrete, externally tunable interaction sites. The ability of poly(N-isopropylacrylamide) (PNIPAM) and poly(N-isopropylmethacrylamide) (PNIPMAM) microgels to adsorb to the oil/water (O/W) interface and create Pickering-stabilized mini-emulsions was first tested using the controlled addition of sub-micron-sized polydimethylsiloxane (PDMS) oil droplets to a microgel suspension. The use of a mixture of PNIPAM and PNIPMAM microgels differing in size and fluorescent labeling then resulted in the formation of thermosensitive patchy particles, where the patches can be visualised using fluorescence confocal laser scanning microscopy. The size of the assembled decorated droplets and the number of adsorbed microgels was further reduced using an in situ synthesis approach, where the oil droplets are directly synthesised in the presence of microgels. This results in the formation of highly monodisperse microgel-decorated PDMS oil droplets with a small number of microgels adsorbed to the droplet interface. We demonstrate that we can use temperature to change the interaction potential between these interaction sites and thus trigger a reversible association of the individual decorated droplets at temperatures above the volume phase transition temperature TVPT of the microgels. Finally, we investigated the temporal evolution of the decorated droplets and found that small and well-defined clusters of microgels form in the early stages of the process primarily through the action of capillary forces. These clusters mimic colloidal molecules with a small number of discrete and thermosensitive binding sites.