Morphology of polymer brushes infiltrated by attractive nanoinclusions of various sizes

Adhesion dynamics of Janus nanocarriers to endothelial cells: A dissipative particle dynamics study

Janus nanocarriers (NCs) provide promising features in interfacial applications such as targeted drug delivery. Herein, we use dissipative particle dynamics simulations to study the adhesion dynamics of NCs with Janus ligand compositions to the endothelial cell as a function of a series of effects, such as the initial orientation, ligand density, shape, and size of Janus NCs. The Janus NCs, with its long axis parallel to the endothelial glycocalyx (EG) layer, has the best penetration depth due to its lower potential energy and the lowest shell entropy loss. Among different shapes of Janus NCs, both the potential energy and the EG entropy loss control the penetration. In fact, at the parallel orientations, Janus shapes with a robust mechanical strength and larger surface area at the EG/water interface can rotate and penetrate more efficiently. An increase in the ligand density of Janus NCs increases entropy losses of both the hydrophilic and the hydrophobic ligands and decreases the potential energy. Thus, for a specific Janus NCs, functionalizing with an appropriate ligand density would help driving forces prevail over barriers of penetration into the EG layer. For a particular ligand density, once the radius of the Janus NCs exceeds the appropriate size, barriers such as hydrophobic ligands and shell entropy losses are also reinforced significantly and surpass driving forces. Our observations reveal that entropy losses for hydrophobic ligands of Janus NCs and for the shell of NCs are decisive for the adhesion and penetration of Janus NCs to endothelial cells.

Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex

As the main gatekeeper of the nucleocytoplasmic transport in eukaryotic cells, the nuclear pore complex (NPC) faces the daunting task of facilitating the bidirectional transport of a high volume of macromolecular cargoes while ensuring the selectivity, speed, and efficiency of this process. The competition between opposing nuclear import and export fluxes passing through the same channel is expected to pose a major challenge to transport efficiency. It has been suggested that phase separation-like radial segregation of import and export fluxes within the assembly of intrinsically disordered proteins that line the NPC pore could be a mechanism for ensuring efficient bidirectional transport. We examine the impact of radial segregation on the efficiency of bidirectional transport through the NPC using a coarse-grained computational model of the NPC. We find little evidence that radial segregation improves transport efficiency. By contrast, surprisingly, we find that NTR crowding may enhance rather than impair the efficiency of bidirectional transport although it decreases the available space in the pore. We identify mechanisms of this novel crowding-induced transport cooperativity through the self-regulation of cargo density and flux in the pore. These findings explain how the functional architecture of the NPC resolves the problem of efficient bidirectional transport, and provide inspiration for the alleviation of clogging in artificial selective nanopores.

Effects of Sequence Composition, Patterning and Hydrodynamics on the Conformation and Dynamics of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling. Unlike the well-defined structures of the classical natively folded proteins, IDPs and IDRs dynamically span large conformational and structural ensembles. This dynamic disorder impedes the study of the relationship between the amino acid sequences of the IDPs and their spatial structures and dynamics, with different experimental techniques often offering seemingly contradictory results. Although experimental and theoretical evidence indicates that some IDP properties can be understood based on their average biophysical properties and amino acid composition, other aspects of IDP function are dictated by the specifics of the amino acid sequence. We investigate the effects of several key variables on the dimensions and the dynamics of IDPs using coarse-grained polymer models. We focus on the sequence "patchiness" informed by the sequence and biophysical properties of different classes of IDPs-and in particular FG nucleoporins of the nuclear pore complex (NPC). We show that the sequence composition and patterning are well reflected in the global conformational variables such as the radius of gyration and hydrodynamic radius, while the end-to-end distance and dynamics are highly sequence-specific. We find that in good solvent conditions highly heterogeneous sequences of IDPs can be well mapped onto averaged minimal polymer models for the purpose of prediction of the IDPs dimensions and dynamic relaxation times. The coarse-grained simulations are in a good agreement with the results of atomistic MD. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for the further applications of mesoscopic models of FG nucleoporins and IDPs more broadly.

Morphology of Polymer Brushes in the Presence of Attractive Nanoparticles: Effects of Temperature

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.

Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage

Nuclear pore complexes (NPCs) discriminate nonspecific macromolecules from importin and exportin receptors, collectively termed “karyopherins” (Kaps), that mediate nucleocytoplasmic transport. This selective barrier function is attributed to the behavior of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups) that guard the NPC channel. However, NPCs in vivo are typically enriched with different Kaps, and how they impact the NPC barrier remains unknown. Here, we show that two major Kaps, importinβ1/karyopherinβ1 (Kapβ1) and exportin 1/chromosomal maintenance 1 (CRM1), are required to fortify NPC barrier function in vivo. Their enrichment at the NPC is sustained by promiscuous binding interactions with the FG Nups, which enable CRM1 to compensate for the loss of Kapβ1 as a means to maintain NPC barrier function. However, such a compensatory mechanism is constrained by the cellular abundances and different binding kinetics for each respective Kap, as evidenced for importin-5. Consequently, we find that NPC malfunction and nucleocytoplasmic leakage result from poor Kap enrichment.

Kinetics of high density functional polymer nanocomposite formation by tuning enthalpic and entropic barriers

High density functional polymer nanocomposites (PNCs) with high degree of dispersion have recently emerged as novel materials for various thermo-mechanical, optical and electrical applications. The key challenge is to attain a high loading while maintaining reasonable dispersion to attain maximum possible benefits from the functional nanoparticle additives. Here, we report a facile method to prepare polymer grafted nanoparticle (PGNP)-based high density functional polymer nanocomposites using thermal activation of a high density PGNP monolayer to overcome entropic or enthalpic barriers to insertion of PGNPs into the underlying polymer films. We monitor the temperature-dependent kinetics of penetration of a high density PGNP layer and correlate the penetration time to the effective enthalpic/entropic barriers. The experimental results are corroborated by coarse-grained molecular dynamics simulations. Repeated application of the methodology to insert nanoparticles by appropriate control over temperature, time and graft-chain properties can lead to enhanced densities of loading in the PNC. Our method can be engineered to produce a wide range of high density polymer nanocomposite membranes for various possible applications including gas separation and water desalination.

Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment

The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.

Nanoelectrochemical Study of Molecular Transport through the Nuclear Pore Complex

The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates the transport of both small molecules and macromolecules between the nucleus and cytoplasm of a eukaryotic cell to regulate gene expression. In this personal account, we introduce recent progress in our nanoelectrochemical study of molecular transport through the NPC. Our work represents the importance of chemistry in understanding and controlling of NPC-mediated molecular transport to enable the efficient and safe delivery of genetic therapeutics into the nucleus, thereby fundamentally contributing to human health. Specifically, we employ nanoscale scanning electrochemical microscopy to test our hypothesis that the nanopore of the NPC is divided by transport barriers concentrically into peripheral and central routes to efficiently mediate the bimodal traffic of protein transport and RNA export, respectively, through cooperative hydrophobic and electrostatic interactions.

Concentrating Vapor Traces with Binary Brushes of Immiscible Polymers

Vapors in the air around us can provide useful information about our environment, but we need sensitive vapor sensors to access this information, especially because those vapors are often present at very low concentrations. We report molecular dynamics simulations of a concept that can significantly increase the sensitivity of vapor sensors at low concentrations. By coating the sensor surfaces with end-anchored immiscible polymers, surface-bound polymer blends are formed that can concentrate vapors, reaching sorption enhancements of more than one order of magnitude, especially at low vapor concentrations.

Nanopore gates via reversible crosslinking of polymer brushes: a theoretical study

Polymer-brush-modified nanopores are synthetic structures inspired by the gated transport exhibited by their biological counterparts. This work theoretically analyzes how the reversible crosslinking of a polymer network by soluble species can be used to control transport through nanochannels and pores. The study was performed with a molecular theory that allows inhomogeneities in the three spatial dimensions and explicitly takes into account the size, shape and conformations of all molecular species, considers the intermolecular interactions between the polymers and the soluble crosslinkers and includes the presence of a translocating particle inside the pore. It is shown than increasing the concentration of the soluble crosslinkers in bulk solution leads to a gradual increase of its number within the pore until a critical bulk concentration is reached. At the critical concentration, the number of crosslinkers inside the pore increases abruptly. For long chains, this sudden transition triggers the collapse of the polymer brush to the center of the nanopore. The resulting structure increases the free-energy barrier that a translocating particle has to surmount to go across the pore and modifies the route of translocation from the axis of the pore to its walls. On the other hand, for short polymer chains the crosslinkers trigger the collapse of the brush to the pore walls, which reduces the translocation barrier.

Sorption Characteristics of Polymer Brushes in Equilibrium with Solvent Vapors

While polymer brushes in contact with liquids have been researched intensively, the characteristics of brushes in equilibrium with vapors have been largely unexplored, despite their relevance for many applications, including sensors and smart adhesives. Here, we use molecular dynamics simulations to show that solvent and polymer density distributions for brushes exposed to vapors are qualitatively different from those of brushes exposed to liquids. Polymer density profiles for vapor-solvated brushes decay more sharply than for liquid-solvated brushes. Moreover, adsorption layers of enhanced solvent density are formed at the brush–vapor interface. Interestingly and despite all of these effects, we find that solvent sorption in the brush is described rather well with a simple mean-field Flory–Huggins model that incorporates an entropic penalty for stretching of the brush polymers, provided that parameters such as the polymer–solvent interaction parameter, grafting density, and relative vapor pressure are varied individually.

A unified understanding of the cononsolvency of polymers in binary solvent mixtures

The standard random phase approximation (RPA) model is applied to investigate the cononsolvency of polymers in mixtures of two good solvents. It is shown that in the RPA framework, the two types of cononsolvency behaviors reported in previous theoretical studies can be unified under the same concept of mean-field density correlations. The two types of cononsolvency are distinguished by the solvent composition at which maximum immiscibility is predicted to occur. The maximum immiscibility occurs with the cosolvent being the minor solvent if the driving mechanism is the preferential solvation of polymers. For the cononsolvency driven by the preferential mixing of solvents, the maximum immiscibility is predicted at a symmetric solvent composition. An interplay of the two driving forces gives rise to a reentrant behavior in which the cononsolvency of the two types switches from one to the other, through a "conventional" region where the overall solvent quality varies monotonically with the solvent composition. The RPA model developed in this work provides a unified analytical framework for understanding the conformational and solubility transition of polymers in multi-solvent mixtures. Such findings highlight the complex role played by the solvents in polymer solutions, a problem of fundamental and practical interest in diverse applications of materials science.

The Role of Cohesiveness in the Permeability of the Spatial Assemblies of FG Nucleoporins

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.

Controlling the Surface Properties of Binary Polymer Brush-Coated Colloids via Targeted Nanoparticles

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.

Synergistic Effects of Bound Micelles and Temperature on the Flexibility of Thermoresponsive Polymer Brushes

The persistence length is a key parameter for the quantitative interpretation of the flexibility of polymers. We have studied complexes composed of a spherical poly(N-isopropylacrylamide) (PNIPAM) brush and a sodium dodecyl sulfate micelle in an effort to characterize the flexibility of tethered PNIPAM below the lower critical solution temperature T_LCST. An analytical mean-field model is used to describe the persistence length L_p in a broad range of ψ, the number of bound micelles per chain. The persistence length of micelle-constrained PNIPAM is quantitatively correlated with the thermal energy k_BT, electrostatic repulsion f_C, and effective excluded-volume parameter ν_eff. The persistence length per ψ, which depends on T and f_C, is found to scale with a synergistic effect f_C/(ψk_BT). The results reveal that the bound-micelle charges affecting the persistence length are analogous to the fixed charges of polyelectrolytes, though the bound micelles are separated by a large number of neutral monomers. The extension ⟨L⟩ of micelle-constrained PNIPAM decreases as ⟨L⟩ ∼ f_C^-β_F with f_C, where β_F ≈ 0.58-0.8 depending on ψ, but as the universal power law ⟨L⟩ ∼ (f_C/k_BT)^-0.6 with the synergistic effect f_C/(k_BT), irrespective of ψ. In spite of the intricate interplay among the multiple components in the system, the extension scales as a function of ν_eff as ⟨L⟩ ∼ (ν_eff/ψL_p)^-β_V, where β_V ≈ 0.35 for the significant monomer interaction and β_V ≈ 0.2 for the weak or negligible monomer interaction.

How to operate a nuclear pore complex by Kap-centric control

Nuclear pore complexes (NPCs) mediate molecular transport between the nucleus and cytoplasm in eukaryotic cells. Tethered within each NPC lie numerous intrinsically disordered proteins known as FG nucleoporins (FG Nups) that are central to this process. Over two decades of investigation has converged on a view that a barrier mechanism consisting of FG Nups rejects non-specific macromolecules while promoting the speed and selectivity of karyopherin (Kaps) receptors (and their cargoes). Yet, the number of NPCs in the cell is exceedingly small compared to the number of Kaps, so that in fact there is a high likelihood the pores are always populated by Kaps. Here, we contemplate a view where Kaps actively participate in regulating the selectivity and speed of transport through NPCs. This so-called "Kap-centric" control of the NPC accounts for Kaps as essential barrier reinforcements that play a prerequisite role in facilitating fast transport kinetics. Importantly, Kap-centric control reconciles both mechanistic and kinetic requirements of the NPC, and in so doing potentially resolves incoherent aspects of FG-centric models. On this basis, we surmise that Kaps prime the NPC for nucleocytoplasmic transport by fine-tuning the NPC microenvironment according to the functional needs of the cell.

Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

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.

DOI:http://dx.doi.org/10.7554/eLife.10785.001

Animal, plant and fungal cells contain a structure called the nucleus, inside which the genetic material of the cell is stored. For the cell to work properly, certain proteins and other molecules need to be able to enter and exit the nucleus. This transport is carried out by pore-like molecular “devices” known as Nuclear Pore Complexes, whose architecture and mode of operation are unique among cellular transporters.

Nuclear Pore Complexes are charged with a daunting task of deciding which of the hundreds of molecules it conducts per second should go through and which should not. Small molecules can pass freely through Nuclear Pore Complexes. However, larger molecules can only pass through the pore efficiently if they are bound to specialized transport proteins that interact with the proteins – called FG nucleoporins – that line the pore. A unique feature of the FG nucleoporins is that, unlike typical proteins, they do not have a defined three-dimensional structure. Instead, they form a soft and pliable lining inside the Nuclear Pore Complex passageway.

Exactly how interacting with transport proteins affects the structure and spatial arrangements of the FG nucleoporins in a way that allows them to control transport is not well understood. This is in part because existing experimental techniques are unable to study the structures of the FG nucleoporins in enough detail to track how they change during transport. The complexity and the diversity of the FG nucleoporins also make them difficult to model in detail.

Vovk, Gu et al. have developed a theoretical model that is based on just three basic physical properties of the FG nucleoporins – their flexibility, their ability to interact with each other, and their binding with the transport proteins. Future work can refine the model by incorporating further molecular details about the interactions between FG nucleoporins and transport proteins.

The predictions made by this simple model agree well with experimental results in a wide range of situations – from single molecules to complex spatial assemblies. They also explain why some of the experimental results appear to contradict each other and suggest how several outstanding controversies in the field can be reconciled. Because the model invokes only fundamental physical principles of FG nucleoporin assemblies, it shows that some of their general properties do not depend on the exact conditions. In particular, this might shed light on why Nuclear Pore Complexes in different organisms perform essentially the same function, although the details of their molecular structure may differ. This also suggests how the FG nucleoporins can be manipulated to build artificial devices based on the same principles.

DOI:http://dx.doi.org/10.7554/eLife.10785.002

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.

Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches

Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.

Positron annihilation spectroscopy: a new frontier for understanding nanoparticle-loaded polymer brushes

Nanoparticle-loaded polymer brushes are powerful tools for the development of innovative devices. However, their characterization is challenging and arrays of different techniques are typically required to gain sufficient insight. Here we demonstrate for the first time the suitability of positron annihilation spectroscopy (PAS) to investigate, with unprecedented detail and without making the least damage to samples, the physico-chemical changes experienced by pH-responsive polymer brushes after protonation and after loading of silver nanoparticles. One of the most important findings is the depth profiling of silver nanoparticles inside the brushes. These results open up a completely new way to understand the structure and behavior of such complex systems.

Promiscuous binding of Karyopherinβ1 modulates FG nucleoporin barrier function and expedites NTF2 transport kinetics

The transport channel of nuclear pore complexes (NPCs) contains a high density of intrinsically disordered proteins that are rich in phenylalanine-glycine (FG)-repeat motifs (FG Nups). The FG Nups interact promiscuously with various nuclear transport receptors (NTRs), such as karyopherins (Kaps), that mediate the trafficking of nucleocytoplasmic cargoes while also generating a selectively permeable barrier against other macromolecules. Although the binding of NTRs to FG Nups increases molecular crowding in the NPC transport channel, it is unclear how this impacts FG Nup barrier function or the movement of other molecules, such as the Ran importer NTF2. Here, we use surface plasmon resonance to evaluate FG Nup conformation, binding equilibria, and interaction kinetics associated with the multivalent binding of NTF2 and karyopherinβ1 (Kapβ1) to Nsp1p molecular brushes. NTF2 and Kapβ1 show different long- and short-lived binding characteristics that emerge from varying degrees of molecular retention and FG repeat binding avidity within the Nsp1p brush. Physiological concentrations of NTF2 produce a collapse of Nsp1p brushes, whereas Kapβ1 binding generates brush extension. However, the presence of prebound Kapβ1 inhibits Nsp1p brush collapse during NTF2 binding, which is dominated by weak, short-lived interactions that derive from steric hindrance and diminished avidity with Nsp1p. This suggests that binding promiscuity confers kinetic advantages to NTF2 by expediting its facilitated diffusion and reinforces the proposal that Kapβ1 contributes to the integral barrier function of the NPC.

A Polymer-Brush-Based Nanovalve Controlled by Nanoparticle Additives: Design Principles

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.

Probing the disordered domain of the nuclear pore complex through coarse-grained molecular dynamics simulations

The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC.

Karyopherin-centric control of nuclear pores based on molecular occupancy and kinetic analysis of multivalent binding with FG nucleoporins

Intrinsically disordered Phe-Gly nucleoporins (FG Nups) within nuclear pore complexes exert multivalent interactions with transport receptors (Karyopherins (Kaps)) that orchestrate nucleocytoplasmic transport. Current FG-centric views reason that selective Kap translocation is promoted by alterations in the barrier-like FG Nup conformations. However, the strong binding of Kaps with the FG Nups due to avidity contradicts rapid Kap translocation in vivo. Here, using surface plasmon resonance, we innovate a means to correlate in situ mechanistic (molecular occupancy and conformational changes) with equilibrium (binding affinity) and kinetic (multivalent binding kinetics) aspects of Karyopherinβ1 (Kapβ1) binding to four different FG Nups. A general feature of the FxFG domains of Nup214, Nup62, and Nup153 is their capacity to extend and accommodate large numbers of Kapβ1 molecules at physiological Kapβ1 concentrations. A notable exception is the GLFG domain of Nup98, which forms a partially penetrable cohesive layer. Interestingly, we find that a slowly exchanging Kapβ1 phase forms an integral constituent within the FG Nups that coexists with a fast phase, which dominates transport kinetics due to limited binding with the pre-occupied FG Nups at physiological Kapβ1 concentrations. Altogether, our data reveal an emergent Kap-centric barrier mechanism that may underlie mechanistic and kinetic control in the nuclear pore complex.

Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy

Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.