We study the role of temperature on the structure of pure polymer brushes and their mixture with attractive nanoparticles in flat and cylindrical geometries. It has previously been established that ...the addition of such nanoparticles causes the polymer brush to collapse and the intensity of the collapse depends on the attraction strength, the nanoparticle diameter, and the grafting density. In this work, we carry out molecular dynamics simulation under good solvent conditions to show how the collapse transition is affected by the temperature, for both plane grafted and inside-cylinder grafted brushes. We first examine the pure brush morphology and verify that the brush height is insensitive to temperature changes in both planar and cylindrical geometries, as expected for a polymer brush in a good solvent. On the other hand, for both system geometries, the brush structure in the presence of attractive nanoparticles is quite responsive to temperature changes. Generally speaking, for a given nanoparticle concentration, increasing the temperature causes the brush height to increase. A brush which contracts when nanoparticles are added eventually swells beyond its pure brush height as the system temperature is increased. The combination of two easily controlled external parameters, namely, concentration of nanoparticles in solution and temperature, allows for sensitive and reversible adjustment of the polymer brush height, a feature which could be exploited in designing smart polymer devices.
Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate ...competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry.
Nuclear pore complexes (NPCs) conduct selective, bidirectional transport across the nuclear envelope. The NPC passageway is lined by intrinsically disordered proteins that contain hydrophobic ...phenylalanine-glycine (FG) motifs, known as FG nucleoporins (FG nups), that play the key role in the NPC transport mechanism. Cohesive interactions among the FG nups, which arise from the combination of hydrophobic, electrostatic, and other forces, have been hypothesized to control the morphology of the assemblies of FG nups in the NPC, as well as their permeability with respect to the transport proteins. However, the role of FG nup cohesiveness is still vigorously debated. Using coarse-grained polymer theory and numerical simulations, we study the effects of cohesiveness on the selective permeability of in vitro FG nup assemblies in different geometries that have served as proxies for the morphological and transport properties of the NPC. We show that in high-density FG nup assemblies, increase in cohesiveness leads to the decrease in their permeability, in accordance with the accepted view. On the other hand, the permeability of low-density assemblies is a nonmonotonic function of the cohesiveness, and a moderate increase in cohesiveness can enhance permeability. The density- and cohesiveness-dependent effects on permeability are explained by considering the free-energy cost associated with penetrating the FG nup assemblies. We discuss the implications of these findings for the organization and function of the NPC.
Characterization of the interactions between nanosize ligands and polymeric substrates is important for predictive design of nanomaterials and in biophysical applications. The multivalent nature of ...the polymer–nanoparticle interaction and the dynamics of multiple internal conformations of the polymer chains makes it difficult to infer microscopic interactions from macroscopic binding assays. Using coarse-grained simulations, we estimate the free energy of binding between a nanoparticle and a surface-grafted polymeric substrate as a function of pertinent parameters such as polymer chain length, nanoparticle size, and microscopic polymer–nanoparticle attraction. We also investigate how the presence of the nanoparticle affects the internal configurations of the polymeric substrate, and estimate the entropic cost of binding. The results have important implications for the understanding of complex macromolecular assemblies.
Polymer-grafted surfaces and channels are increasingly used for the design of responsive materials and sensors due to robust performance and ease of use. Various strategies for the control of the ...nanoscale morphologies of such materials and devices are being tested. Entropic repulsion between the polymer chains in a grafted brush of sufficient density causes the chains to extend in the direction perpendicular to the grafting surface in comparison to the position of unattached polymers. When nanoparticles having attractive interactions with the polymers are introduced into the solvent, these nanoparticles tend to infiltrate into the brush and reduce its extension. Under certain conditions, a sharp reduction in brush height extension can occur over a narrow range of nanoparticle concentrations in solution. We describe a way of controlling transport through polymer-functionalized nanochannels with nanoparticle additives, relying on the physics of nanoparticles and polymer brushes under confinement, and we suggest a blueprint for the creation of a tunable nanovalve. The nanovalve is modeled as a cylinder with a polymer brush grafted on its inside surface. Brush properties such as the chain length and the grafting density are chosen so that the brush chains extend into the center of the cylinder in the absence of nanoparticles, occluding the flux of analyte molecules through the pore. When nanoparticles that are attracted to the polymers are introduced into solution, they infiltrate into the brush and partially collapse it against the cylindrical grafting surface, opening space in the center of the cylinder through which analyte molecules can flow. The operation of such a nanovalve is analyzed via self-consistent field theory calculations in the strong-stretching approximation. Self-consistent field analysis is supported by Langevin dynamics simulations of the underlying coarse-grained model of the polymer–nanoparticle system.
This paper explores a novel mechanism for controlling the surface properties of polymer-coated colloids using targeted (“sticky”) nanoparticles which attract monomers of certain polymer species. In ...our study, colloids are coated by two types of tethered polymer chains having different chemical properties. Attraction of nanoparticles to the monomers of one polymer type causes these polymer chains to contract toward the grafting surface, rendering the other type more exposed to the environment. Thus, the effective surface properties of the colloid are dominated by the intended polymer type. We use coarse-grained molecular dynamics (CGMD) simulation to demonstrate that introducing nanoparticles which interact preferentially with certain types of polymers makes it possible to switch between different surface properties of the colloid. This mechanism can in principle be exploited in drug delivery systems and self-assembly applications.
Paracellular ion transport in epithelia is mediated by pores formed by members of the claudin family. The degree of selectivity and the molecular mechanism of ion permeation through claudin pores are ...poorly understood. By expressing a high-conductance claudin isoform, claudin-2, in high-resistance Madin-Darby canine kidney cells under the control of an inducible promoter, we were able to quantitate claudin pore permeability. Claudin-2 pores were found to be narrow, fluid filled, and cation selective. Charge selectivity was mediated by the electrostatic interaction of partially dehydrated permeating cations with a negatively charged site within the pore that is formed by the side chain carboxyl group of aspartate-65. Thus, paracellular pores use intrapore electrostatic binding sites to achieve a high conductance with a high degree of charge selectivity.
Addition of nanoparticles can control the morphologies of grafted polymer layers that are important in a variety of natural and artificial systems. We study the morphologies of grafted polymer layers ...interacting attractively with nanoparticle inclusions, as a function of particle size and the interaction strength, using self-consistent field theory and Langevin dynamics simulations. We find that the addition of nanoparticles causes distinctive changes in the layer morphology. For sufficiently strong interaction/binding, increasing the concentration of nanoparticles causes a compression of the polymer layer into a compact, low height state, followed by a subsequent rebound and swelling at sufficiently high concentrations. For nanoparticles of small size, the compression of the layer is sharp and occurs over a narrow range of nanoparticle concentrations. The transition region widens as the nanoparticle size increases. The transition is initiated via a dense layer of tightly bound monomers and nanoparticles near the grafting surface, with a low density region above it. For nanoparticles much larger than the characteristic graft spacing in the brush, the behavior is reversed: the nanoparticles penetrate only the dilute region near the top of the polymer layer without causing the layer to collapse.
Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC ...transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function.
PDF
