Biology subjects

Zilman, A.

Publications and source records attributed to Zilman, A..

8 recordsLinked to original sources

bioRxiv2024

Ligand induced receptor multimerization achieves the specificity enhancement of kinetic proofreading without associated costs

Kinetic proofreading (KPR) is a commonly invoked mechanism for specificity enhancement of receptor signaling. However, specificity enhancement comes at a cost of non-equilibrium energy input and signal attenuation. We show that ligand induced multimeric receptor assembly can enhance receptor specificity to the same degree as KPR, yet without the need for out-of-equilibrium energy expenditure and signal loss. We show how multimeric receptor specificity enhancement arises from the amplification of affinity differences via sequential progression down a free energy landscape. We also show that multimeric receptor ligand recognition is more robust to stochastic fluctuations and molecular noise than KPR receptors. Finally, we show that multimeric receptors perform signaling tasks beyond specificity enhancement like absolute discrimination and aspects of ligand antagonism. Our results suggest that multimeric receptors may serve as a potent mechanism of ligand discrimination comparable to and potentially with more advantages than traditional proofreading.

biophysics↗

bioRxiv2024

Specificity and tunability of efflux pumps: a new role for the proton gradient?

Bacterial efflux pumps that transport antibacterial drugs out of the bacterial cells have broad specificity, commonly leading to broad spectrum resistance and limiting treatment strategies for infections. It remains unclear how efflux pumps can maintain this broad spectrum specificity to diverse drug molecules while limiting the efflux of other cytoplasmic content. We investigate the origins of this broad specificity using theoretical models informed by the experimentally determined structural and kinetic properties of efflux pumps. We develop a set of mathematical models describing operation of efflux pumps as a discrete cyclic stochastic process across a network of states characterizing pump conformations and the presence/absence of bound ligands and protons. We find that the pump specificity is determined not solely by the drug affinity to the pump-as is commonly assumed-but it is also directly affected by the periplasmic pH and the transmembrane potential. Therefore, the pump effectiveness in removing a particular drug molecule from the cell can be tuned by modifying the proton concentration gradient and the voltage drop across the membrane. Furthermore, we find that while both the proton concentration gradient across the membrane and the transmembrane potential contribute to the thermodynamic force driving the pump, their effects on the efflux enter not strictly in a combined proton motive force, but rather they have two distinguishable effects on the overall throughput. These results potentially explain the broad specificity of efflux pumps and suggest ways to overcome bacterial resistance, while highlighting unexpected effects of thermodynamic driving forces out of equilibrium.

biophysics↗

bioRxiv2023

Mechanics limit ecological diversity and promote heterogeneity in confined bacterial communities

Multi-species bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here we study a model system consisting of two populations of non-motile E. coli bacteria competing within open, monolayer micro-channels. The competitive dynamics is observed to be bi-phasic: after seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Polya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.

biophysics↗

bioRxiv2023

Proofreading Is Too Noisy For Effective Ligand Discrimination

Kinetic proofreading (KPR) has been used as a paradigmatic explanation for the high specificity of important biological processes including ligand discrimination by cellular receptors. Kinetic proofreading enhances the difference in the mean receptor occupancy between different ligands, thus potentially enabling better discrimination. On the other hand, proofreading also attenuates the signal, increasing the relative magnitude of noise in the downstream signal. This can interfere with reliable ligand discrimination. To understand the effect of noise on ligand discrimination beyond the comparison of the mean signals, we formulate the task of ligand discrimination as a problem of statistical estimation of the molecular affinity of ligands. Our analysis reveals that proofreading typically worsens ligand resolution which decreases with the number of proofreading steps under most commonly considered conditions. This contrasts with the usual notion that kinetic proofreading universally improves ligand discrimination with additional proofreading steps. Our results are consistent across a variety of different proofreading schemes, suggesting that they are inherent to the KPR mechanism itself rather than any particular model of molecular noise. Based on our results, we suggest alternative roles for kinetic proofreading schemes such as multiplexing and combinatorial encoding in multi-ligand/multi-output pathways.

biophysics↗

bioRxiv2023

Spatial exclusion leads to tug-of-war ecological dynamics between competing species within microchannels

Competition is ubiquitous in microbial communities, shaping both their spatial and temporal structure and composition. Many classic minimal models, such as the Moran model, have been employed in ecology and evolutionary biology to understand the role of fixation and invasion in the maintenance of a population. Informed by recent experimental studies of cellular competition in confined spaces, we extend the Moran model to explicitly incorporate spatial exclusion through mechanical interactions among cells within a one-dimensional, open microchannel. The results of our spatial exclusion model differ significantly from those of its classical counterpart. The fixation/extinction probability of a species sharply depends on the species initial relative abundance, and the mean time to fixation is greatly accelerated, scaling logarithmically, rather than algebraically, with the system size. In non-neutral cases, spatial exclusion tends to attenuate the effects of fitness differences on the probability of fixation, and the fixation times increase as the relative fitness differences between species increase. Successful fixation by invasive species, whether through mutation or immigration, are also less probable on average than in the Moran model. Surprisingly, in the spatial exclusion model, successful fixations occur on average more rapidly in longer channels. The mean time to fixation heuristically arises from the boundary between populations performing either quasi-neutral diffusion, near a semi-stable fixed point, or quasi-deterministic avalanche dynamics away from the fixed point. These results, which can be tested in microfluidic monolayer devices, have implications for the maintenance of species diversity in dense bacterial ecosystems where spatial exclusion is central to the competition, such as in organized biofilms or intestinal crypts. The results may be broadly applied to any system displaying tug-of-war type dynamics with a region of quasi-neutral diffusion centered around regions of deterministic population collapse. Author summaryCompetition for territory between different species has far reaching consequences for the diversity and fate of bacterial communities. In this study, we theoretically and computationally study the competitive dynamics of two bacterial populations competing for space in confined environments. The model we develop extends classical models that have served as paradigms for understanding competitive dynamics but did not explicitly include spatial exclusion. We find that spatial effects drastically change the probability of one species successfully outcompeting the other and accelerates the mean time it takes for a species to exclude the other from the environment. In comparison to the predictions of population models that neglect spatial exclusion, species with higher selective advantages are less heavily favoured to outcompete their rival species. Moreover, spatial exclusion influences the success of an invasive species taking over a densely populated community. Compared to classical well-mixed models, there is a reduction in the effectiveness of an invaders fitness advantage at improving the chances of taking over the population. Our results show that spatial exclusion has rich and unexpected repercussions on species dominance and the long-time composition of populations. These must be considered when trying to understand complex bacterial ecosystems such as biofilms and intestinal flora.

ecology↗

bioRxiv2022

Self-regulation of the nuclear pore complex enables clogging-free crowded transport

Nuclear pore complexes (NPCs) are the main conduits for macromolecular transport into and out of the nucleus of eukaryotic cells. The central component of the NPC transport mechanism is an assembly of intrinsically disordered proteins (IDPs) that fills the NPC channel. The channel interior is further crowded by large numbers of simultaneously translocating cargo-carrying and free transport proteins. How the NPC can efficiently, rapidly and selectively transport varied cargoes in such crowded conditions remains ill understood. Past experimental results suggest that the NPC is surprisingly resistant to clogging and that transport may even become faster and more efficient as the concentration of transport protein increases. To understand the mechanisms behind these puzzling observations, we construct a computational model of the NPC comprising only a minimal set of commonly-accepted consensus features. This model qualitatively reproduces the previous experimental results and identifies self-regulating mechanisms that relieve crowding. We show that some of the crowding-alleviating mechanisms - such as preventing saturation of the bulk flux - are "robust" and rely on very general properties of crowded dynamics in confined channels, pertaining to a broad class of selective transport nanopores. By contrast, the counter-intuitive ability of the NPC to leverage crowding to achieve more efficient single molecule translocation is "fine-tuned" and relies on the particular spatial architecture of the IDP assembly in the NPC channel.

biophysics↗

bioRxiv2020

Physical modelling of multivalent interactions in the nuclear pore complex

In the nuclear pore complex (NPC), intrinsically disordered proteins (FG Nups) along with their interactions with more globular proteins called nuclear transport receptors (NTRs) are vital to the selectivity of transport into and out of the cell nucleus. While such interactions can be modelled at different levels of coarse graining, in-vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, where the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and non-cohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity at a level of minimal complexity, and compare them to experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs plays a minor role for their equilibrium binding properties, but is of significance when it comes to (un)binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.

biophysics↗

bioRxiv2020

Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins

Unlike the well defined structures of classical natively folded proteins, Intrinsically Disordered Proteins (IDP) and Intrinsically Disordered Regions (IDR) 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, dynamics, and function. Multiple experimental and theoretical evidence points in many cases to the overall importance of the general properties of the amino acid sequence of the IPDs rather than their precise atomistic details. However, while different experimental techniques can probe aspects of the IDP conformations, often different techniques or conditions offer seemingly contradictory results. Using coarse-grained polymer models informed by experimental observations, we investigate the effects of several key variables on the dimensions and the dynamics of IDPs. The coarse-grained simulations are in a good agreement with the results of atomistic MD. 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 identify the conditions that allow mapping of highly heterogeneous sequences of IDPs onto averaged minimal polymer models. We discuss the implications of these results for the interpretation of the recent experimental measurements, and for further development of appropriate mesoscopic models of IDPs.

biophysics↗