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.

Spiral wave chimeras in complex oscillatory and chaotic systems.

We demonstrate for the first time that spiral wave chimeras-spiral waves with spatially extended unsynchronzied cores-can exist in complex oscillatory and even locally chaotic homogeneous systems under nonlocal coupling. Using ideas from phase synchronization, we show in particular that the unsynchronized cores exhibit a distribution of different frequencies, thus generalizing the main concept of chimera states beyond simple oscillatory systems. In contrast to simple oscillatory systems, we find that spiral wave chimeras in complex oscillatory and locally chaotic systems are characterized by the presence of synchronization defect lines (SDLs), along which the dynamics follows a periodic behavior different from that of the bulk. Whereas this is similar to the case of local coupling, the type of the prevailing SDLs is very different.

Free Energy of Nanoparticle Binding to Multivalent Polymeric Substrates.

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.

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.