Design principles of selective transport through biopolymer barriers

Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups

Macromolecules are transported through the nuclear pore complex (NPC) via a series of transient binding and unbinding events with FG-Nups, which are intrinsically disordered proteins anchored to the pore's inner wall. Prior studies suggest that the weak and transient nature of this binding is crucial for maintaining the transported molecules' diffusivity. In this study, we explored the relationship between binding kinetics and transport efficiency using Brownian dynamics simulations. Our results indicate that the duration of binding is a critical factor in regulating transport efficiency. Specifically, excessively short binding durations insufficiently facilitate transport, while overly long durations impede molecular movement. We calculated the optimal binding duration for efficient molecular transport and found that it aligns with other theoretical predictions. Additionally, the calculated value is comparable to experimental measurements of the association timescale between nuclear transport receptors and FG-Nups at a single binding site. Our study provides a quantitative framework that bridges local molecular interactions with overall transport dynamics through the NPC, offering valuable insights into the mechanisms governing selective molecular transport.

From Static to Dynamic: A Review on the Role of Mucus Heterogeneity in Particle and Microbial Transport

Mucus layers (McLs) are on the front line of the human defense system that protect us from foreign abiotic/biotic particles (e.g., airborne virus SARS-CoV-2) and lubricates our organs. Recently, the impact of McLs on human health (e.g., nutrient absorption and drug delivery) and diseases (e.g., infections and cancers) has been studied extensively, yet their mechanisms are still not fully understood due to their high variety among organs and individuals. We characterize these variances as the heterogeneity of McLs, which lies in the thickness, composition, and physiology, making the systematic research on the roles of McLs in human health and diseases very challenging. To advance mucosal organoids and develop effective drug delivery systems, a comprehensive understanding of McLs' heterogeneity and how it impacts mucus physiology is urgently needed. When the role of airway mucus in the penetration and transmission of coronavirus (CoV) is considered, this understanding may also enable a better explanation and prediction of the CoV's behavior. Hence, in this Review, we summarize the variances of McLs among organs, health conditions, and experimental settings as well as recent advances in experimental measurements, data analysis, and model development for simulations.

On the nuclear pore complex and its emerging role in cellular mechanotransduction

The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm and the nucleus. The NPC controls the nucleocytoplasmic transport by selectively allowing cargoes such as proteins and mRNA to pass through its central channel, thereby playing a vital role in protecting the nuclear component and regulating gene expression and protein synthesis. The selective transport through the NPC originates from its exquisite molecular structure featuring a large scaffold and the intrinsically disordered central channel domain, but the exact mechanism underlying the selective transport remains elusive and is the subject of various, often conflicting, hypotheses. Moreover, recent studies have suggested a new role for the NPC as a mechanosensor, where the NPC changes its channel diameter depending on the nuclear envelope tension, altering the molecular transportability through this nanopore. In this mini-review, we summarize the current understandings of the selective nature of the NPC and discuss its emerging role in cellular mechanotransduction.

Mechanics of 3D Cell-Hydrogel Interactions: Experiments, Models, and Mechanisms

Hydrogels are highly water-swollen molecular networks that are ideal platforms to create tissue mimetics owing to their vast and tunable properties. As such, hydrogels are promising cell-delivery vehicles for applications in tissue engineering and have also emerged as an important base for ex vivo models to study healthy and pathophysiological events in a carefully controlled three-dimensional environment. Cells are readily encapsulated in hydrogels resulting in a plethora of biochemical and mechanical communication mechanisms, which recapitulates the natural cell and extracellular matrix interaction in tissues. These interactions are complex, with multiple events that are invariably coupled and spanning multiple length and time scales. To study and identify the underlying mechanisms involved, an integrated experimental and computational approach is ideally needed. This review discusses the state of our knowledge on cell-hydrogel interactions, with a focus on mechanics and transport, and in this context, highlights recent advancements in experiments, mathematical and computational modeling. The review begins with a background on the thermodynamics and physics fundamentals that govern hydrogel mechanics and transport. The review focuses on two main classes of hydrogels, described as semiflexible polymer networks that represent physically cross-linked fibrous hydrogels and flexible polymer networks representing the chemically cross-linked synthetic and natural hydrogels. In this review, we highlight five main cell-hydrogel interactions that involve key cellular functions related to communication, mechanosensing, migration, growth, and tissue deposition and elaboration. For each of these cellular functions, recent experiments and the most up to date modeling strategies are discussed and then followed by a summary of how to tune hydrogel properties to achieve a desired functional cellular outcome. We conclude with a summary linking these advancements and make the case for the need to integrate experiments and modeling to advance our fundamental understanding of cell-matrix interactions that will ultimately help identify new therapeutic approaches and enable successful tissue engineering.

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.

Moving while you're stuck: a macroscopic demonstration of an active system inspired by binding-mediated transport in biology

Diffusive motion is typically constrained when particles bind to the medium through which they move. However, when binding is transient and the medium is made of flexible filaments, each association or dissociation event produces a stochastic force that can overcome the medium stickiness and enable motion. This mechanism is amply used by biological systems where the act of balancing binding and displacement robustly achieves key functionalities, including bacterial locomotion or selective active filtering in cells. Here we demonstrate the feasibility of making a dynamic system with macroscopic features, in which analogous binding-mediated motion can be actively driven, precisely tuned, and conveniently studied. We find an optimal binding affinity and number of binding sites for diffusive motion, and an inverse relationship between viscosity and diffusivity.

Stochastically gated diffusion model of selective nuclear transport

Nuclear pore complexes (NPCs) allow the selective exchange of molecules between the cytoplasm and cell nucleus. Although small molecules can diffuse freely through a NPC, the transport of proteins and nucleotides requires association with transport factors (kaps). The latter transiently bind to disordered flexible polymers within the NPC, known collectively as phenylalanine-glycine-nucleoporins (FG-Nups). It has recently been shown that transient binding combined with diffusion in the bound state is a sufficient mechanism for selective transport. However, selectivity is significantly reduced if the mobility of the bound state is too slow. In this paper we formulate the binding-diffusion mechanism of selective transport in terms of a "stochastically gated" diffusion process in which each bound particle undergoes confined diffusion within a subdomain of the NPC. This allows us to make explicit the fact that the diffusion of a particle when bound to a polymer tether is spatially confined rather than simply reduced. We calculate the selectivity of the NPC and explore its dependence on the size of the confinement domains. We then use probabilistic methods to determine the splitting probability and mean first passage time (MFPT) for an individual particle to pass through the pore. Our analysis establishes that spatial confinement can significantly reduce selectivity in a binding-diffusion model, suggesting that other biophysical mechanisms such as interchain transfer are required.

Enhanced Diffusion by Reversible Binding to Active Polymers

Cells are known to use reversible binding to active biopolymer networks to allow diffusive transport of particles in an otherwise impenetrable mesh. We here determine the motion of a particle that experiences random forces during binding and unbinding events while being constrained by attached polymers. Using Monte-Carlo simulations and a statistical mechanics model, we find that enhanced diffusion is possible with active polymers. However, this is possible only under optimum conditions that has to do with the relative length of the chains to that of the plate. For example, in systems where the plate is shorter than the chains, diffusion is maximum when many chains have the potential to bind but few remain bound at any one time. Interestingly, if the chains are shorter than the plate, we find that diffusion is maximized when more active chains remain transiently bound. The model provides insight into these findings by elucidating the mechanisms for binding-mediated diffusion in biology and design rules for macromolecular transport in transient synthetic polymers.

SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins

The periplasmic chaperone network ensures the biogenesis of bacterial outer membrane proteins (OMPs) and has recently been identified as a promising target for antibiotics. SurA is the most important member of this network, both due to its genetic interaction with the β-barrel assembly machinery complex as well as its ability to prevent unfolded OMP (uOMP) aggregation. Using only binding energy, the mechanism by which SurA carries out these two functions is not well-understood. Here, we use a combination of photo-crosslinking, mass spectrometry, solution scattering, and molecular modeling techniques to elucidate the key structural features that define how SurA solubilizes uOMPs. Our experimental data support a model in which SurA binds uOMPs in a groove formed between the core and P1 domains. This binding event results in a drastic expansion of the rest of the uOMP, which has many biological implications. Using these experimental data as restraints, we adopted an integrative modeling approach to create a sparse ensemble of models of a SurA•uOMP complex. We validated key structural features of the SurA•uOMP ensemble using independent scattering and chemical crosslinking data. Our data suggest that SurA utilizes three distinct binding modes to interact with uOMPs and that more than one SurA can bind a uOMP at a time. This work demonstrates that SurA operates in a distinct fashion compared to other chaperones in the OMP biogenesis network.

Bound-State Diffusion due to Binding to Flexible Polymers in a Selective Biofilter

Selective biofilters are used by cells to control the transport of proteins, nucleic acids, and other macromolecules. Biological filters demonstrate both high specificity and rapid motion or high flux of proteins. In contrast, high flux comes at the expense of selectivity in many synthetic filters. Binding can lead to selective transport in systems in which the bound particle can diffuse, but the mechanisms that lead to bound diffusion remain unclear. Previous theory has proposed a molecular mechanism of bound-state mobility based only on transient binding to flexible polymers. However, this mechanism has not been directly tested in experiments. We demonstrate that bound mobility via tethered diffusion can be engineered into a synthetic gel using protein fragments derived from the nuclear pore complex. The resulting bound-state diffusion is quantitatively consistent with theory. Our results suggest that synthetic biological filters can be designed to take advantage of tethered diffusion to give rapid, selective transport.