Orit Peleg

Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex.

The molecular structure of the yeast nuclear pore complex (NPC) and the translocation of model particles have been studied with a molecular theory that accounts for the geometry of the pore and the sequence and anchoring position of the unfolded domains of the nucleoporin proteins (the FG-Nups), which control selective transport through the pore. The theory explicitly models the electrostatic, hydrophobic, steric, conformational, and acid-base properties of the FG-Nups. The electrostatic potential within the pore, which arises from the specific charge distribution of the FG-Nups, is predicted to be negative close to pore walls and positive along the pore axis. The positive electrostatic potential facilitates the translocation of negatively charged particles, and the free energy barrier for translocation decreases for increasing particle hydrophobicity. These results agree with the experimental observation that transport receptors that form complexes with hydrophilic/neutral or positively charged proteins to transport them through the NPC are both hydrophobic and strongly negatively charged. The molecular theory shows that the effects of electrostatic and hydrophobic interactions on the translocating potential are cooperative and nonequivalent due to the interaction-dependent reorganization of the FG-Nups in the presence of the translocating particle. The combination of electrostatic and hydrophobic interactions can give rise to complex translocation potentials displaying a combination of wells and barriers, in contrast to the simple barrier potential observed for a hydrophilic/neutral translocating particle. This work demonstrates the importance of explicitly considering the amino acid sequence and hydrophobic, electrostatic, and steric interactions in understanding the translocation through the NPC.

Morphology control of hairy nanopores.

The properties of polymer layers end-grafted to the inner surface of nanopores connected to solvent reservoirs are studied theoretically as a function of solvent quality and pore geometry. Our systematic study reveals that nanoconfinement is affected by both pore radius and length and that the conformations of the polymer chains strongly depend on their grafting position along the nanopore and on the quality of the solvent. In poor solvent, polymer chains can collapse to the walls, form a compact plug in the pore, or self-assemble into domains of different shape due to microphase separation. The morphology of these domains (aggregates on pore walls or stacked micelles along the pore axis) is mainly determined by the relationship between chain length and pore radius. In other cases the number of aggregates depends on pore length. The presence of reservoirs decreases confinement at pore edges due to the changes in available volume and introduces new organization strategies not available for infinite nanochannels. In good solvent conditions, chains grafted at the pore entrances stretch out of the pore, relieving the internal osmotic pressure and increasing the entropy of the polymers. Our study also addresses the experimentally relevant case of end-grafted chains on the outer walls of the membrane surrounding the nanopore. The effect of these polymer chains on the organization within the nanopore depends on solvent quality. For good solvents the outer chains increase the confinement of the chains at the entrance of the pore; however, the effect does not result in new structures. For poor solvents the presence of the outer polymer layer may lead to changes in the morphology of the microphase-separated domains. Our results show the complex interplay between the different interactions in a confined environment and the need to develop theoretical and experimental tools for their study.

Formation of double helical and filamentous structures in models of physical and chemical gels

This discusses two recent models, one that captures physical network formation starting from the molecular architecture of its constituents and another that contains the basic features of phase separation in cross-linked polymer gels: A) the Janus chain (multibead bead-spring type) model exhibiting semiflexibility and induced curvature and B) a stretched elastic network of Lennard-Jones particles. The length scales and related structures predicted by the two generic models are different. Model B, a generic soft solid model, exhibits hysteresis and the formation of filamentous structures in two dimensions. The Janus chain model A is able to describe the process of the formation of double helical superstructures, will be operated in three dimensions, and its internal parameters are directly deduced from atomistic simulation. Both models rely on classical ingredients which have been separately studied extensively: i) the Lennard-Jones particle system, ii) the elastic solid, and iii) the FENE-B model for semiflexible, finitely extendable nonlinear elastic (FENE) polymer chains. While model A combines i) and iii), model B combines i) and ii). This aspect of technical simplicity, however, is contrasted by the rich phenomenology observed for these models. The Janus model even resolves structure formation on the molecular scale. Intriguingly, the coarse dynamical models capture a wide range of superstructures known for polymeric networks and therefore clearly serve to understand their underlying physical mechanisms.

Fibers with Integrated Mechanochemical Switches: Minimalistic Design Principles Derived from Fibronectin

Inspired by molecular mechanisms that cells exploit to sense mechanical forces and convert them into biochemical signals, chemists dream of designing mechanochemical switches integrated into materials. Using the adhesion protein fibronectin, whose multiple repeats essentially display distinct molecular recognition motifs, we derived a computational model to explain how minimalistic designs of repeats translate into the mechanical characteristics of their fibrillar assemblies. The hierarchy of repeat-unfolding within fibrils is controlled not only by their relative mechanical stabilities, as found for single molecules, but also by the strength of cryptic interactions between adjacent molecules that become activated by stretching. The force-induced exposure of cryptic sites furthermore regulates the nonlinearity of stress-strain curves, the strain at which such fibers break, and the refolding kinetics and fraction of misfolded repeats. Gaining such computational insights at the mesoscale is important because translating protein-based concepts into novel polymer designs has proven difficult.

Filamentous networks in phase-separating two-dimensional gels

We introduce a toy model that contains the basic features of microphase separation in polymer gels: a stretched elastic network of Lennard-Jones particles, studied in two dimensions. When temperature is lowered below some value T*, attraction between particles dominates over both thermal motion and elastic forces, and the network separates into dense domains of filaments connected by three-fold vertices, surrounded by low-density domains in which the network is homogeneously stretched. The length of the filaments decreases and the number of domains increases with decreasing temperature. The system exhibits hysteresis characteristic of first-order phase transitions: pre-formed filaments thin upon heating and eventually melt at a temperature T** (>T*). Although details may vary, the above general features are independent of network topology (square or hexagonal), system size, distribution of spring constants, and perturbations of initial conditions.

Communication: Pair interaction ordering in fluids with random interactions

We use molecular dynamics simulations in 2D to study multi-component systems in the limiting case where all the particles are different (APD). The particles are assumed to interact via Lennard-Jones potentials, with identical size parameters but their pair interaction parameters are generated at random from a uniform or from a peaked distribution. We analyze both the global and the local properties of these systems at temperatures above the freezing transition and find that APD fluids relax into a non-random state characterized by clustering of particles according to the values of their pair interaction parameters (particle-identity ordering).