The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices

Signal integration in chemoreceptor complexes

Motile bacteria use large receptor arrays to detect chemical and physical stimuli in their environment, process this complex information, and accordingly bias their swimming in a direction they deem favorable. The chemoreceptor molecules form tripod-like trimers of receptor dimers through direct contacts between their cytoplasmic tips. A pair of trimers, together with a dedicated kinase enzyme, form a core signaling complex. Hundreds of core complexes network to form extended arrays. While considerable progress has been made in revealing the hierarchical structure of the array, the molecular properties underlying signal processing in these structures remain largely unclear. Here we analyzed the signaling properties of nonnetworked core complexes in live cells by following both conformational and kinase control responses to attractant stimuli and to output-biasing lesions at various locations in the receptor molecule. Contrary to the prevailing view that individual receptors are binary two-state devices, we demonstrate that conformational coupling between the ligand binding and the kinase-control receptor domains is, in fact, only moderate. In addition, we demonstrate communication between neighboring receptors through their trimer-contact domains that biases them to adopt similar signaling states. Taken together, these data suggest a view of signaling in receptor trimers that allows significant signal integration to occur within individual core complexes.

Forceful patterning: theoretical principles of mechanochemical pattern formation

Biological pattern formation is essential for generating and maintaining spatial structures from the scale of a single cell to tissues and even collections of organisms. Besides biochemical interactions, there is an important role for mechanical and geometrical features in the generation of patterns. We review the theoretical principles underlying different types of mechanochemical pattern formation across spatial scales and levels of biological organization.

Immune cells use active tugging forces to distinguish affinity and accelerate evolution

Cells are known to exert forces to sense their physical surroundings for guidance of motion and fate decisions. Here, we propose that cells might do mechanical work to drive their own evolution, taking inspiration from the adaptive immune system. Growing evidence indicates that immune B cells-capable of rapid Darwinian evolution-use cytoskeletal forces to actively extract antigens from other cells' surfaces. To elucidate the evolutionary significance of force usage, we develop a theory of tug-of-war antigen extraction that maps receptor binding characteristics to clonal reproductive fitness, revealing physical determinants of selection strength. This framework unifies mechanosensing and affinity-discrimination capabilities of evolving cells: Pulling against stiff antigen tethers enhances discrimination stringency at the expense of absolute extraction. As a consequence, active force usage can accelerate adaptation but may also cause extinction of cell populations, resulting in an optimal range of pulling strength that matches molecular rupture forces observed in cells. Our work suggests that nonequilibrium, physical extraction of environmental signals can make biological systems more evolvable at a moderate energy cost.

Dependence of protein-induced lipid bilayer deformations on protein shape

Membrane proteins typically deform the surrounding lipid bilayer membrane, which can play an important role in the function, regulation, and organization of membrane proteins. Membrane elasticity theory provides a beautiful description of protein-induced lipid bilayer deformations, in which all physical parameters can be directly determined from experiments. While analytic solutions of protein-induced elastic bilayer deformations are most easily developed for proteins with approximately circular cross sections, structural biology has shown that membrane proteins come in a variety of distinct shapes, with often considerable deviations from a circular cross section. We develop here a boundary value method (BVM) that permits the construction of analytic solutions of protein-induced elastic bilayer deformations for protein shapes with arbitrarily large deviations from a circular cross section, for constant as well as variable boundary conditions along the bilayer-protein interface. We apply this BVM to protein-induced lipid bilayer thickness deformations. Our BVM reproduces available analytic solutions for proteins with circular cross section and yields, for proteins with noncircular cross section, excellent agreement with numerical, finite element solutions. On this basis, we formulate a simple analytic approximation of the bilayer thickness deformation energy associated with general protein shapes and show that, for modest deviations from rotational symmetry, this analytic approximation is in good agreement with BVM solutions. Using the BVM, we survey the dependence of protein-induced elastic bilayer thickness deformations on protein shape, and thus explore how the coupling of protein shape and bilayer thickness deformations affects protein oligomerization and transitions in protein conformational state.

Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions

Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy-driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials—such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer—can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.

Mechanochemical coupling of lipid organization and protein function through membrane thickness deformations

Cell membranes are composed of a great variety of protein and lipid species with distinct unperturbed hydrophobic thicknesses. To achieve hydrophobic matching, the lipid bilayer tends to deform around membrane proteins so as to match the protein hydrophobic thickness at bilayer-protein interfaces. Such protein-induced distortions of the lipid bilayer hydrophobic thickness incur a substantial energy cost that depends critically on the bilayer-protein hydrophobic mismatch, while distinct conformational states of membrane proteins often show distinct hydrophobic thicknesses. As a result, hydrophobic interactions between membrane proteins and lipids can yield a rich interplay of lipid-protein organization and transitions in protein conformational state. We combine here the membrane elasticity theory of protein-induced lipid bilayer thickness deformations with the Landau-Ginzburg theory of lipid domain formation to systematically explore the coupling between local lipid organization, lipid and protein hydrophobic thickness, and protein-induced lipid bilayer thickness deformations in membranes with heterogeneous lipid composition. We allow for a purely mechanical coupling of lipid and protein composition through the energetics of protein-induced lipid bilayer thickness deformations as well as a chemical coupling driven by preferential interactions between particular lipid and protein species. We find that the resulting lipid-protein organization can endow membrane proteins with diverse and controlled mechanical environments that, via protein-induced lipid bilayer thickness deformations, can strongly influence protein function. The theoretical approach employed here provides a general framework for the quantitative prediction of how membrane thickness deformations influence the joint organization and function of lipids and proteins in cell membranes.

Effect of receptor cooperativity on methylation dynamics in bacterial chemotaxis with weak and strong gradient

We study methylation dynamics of the chemoreceptors as an Escherichia coli cell moves around in a spatially varying chemoattractant environment. We consider attractant concentration with strong and weak spatial gradient. During the uphill and downhill motion of the cell along the gradient, we measure the temporal variation of average methylation level of the receptor clusters. Our numerical simulations we show that the methylation dynamics depends sensitively on the size of the receptor clusters and also on the strength of the gradient. At short times after the beginning of a run, the methylation dynamics is mainly controlled by short runs which are generally associated with high receptor activity. This results in demethylation at short times. But for intermediate or large times, long runs play an important role and depending on receptor cooperativity or gradient strength, the qualitative variation of methylation can be completely different in this time regime. For weak gradient, both for uphill and downhill runs, after the initial demethylation, we find methylation level increases steadily with time for all cluster sizes. Similar qualitative behavior is observed for strong gradient during uphill runs as well. However, the methylation dynamics for downhill runs in strong gradient show highly nontrivial dependence on the receptor cluster size. We explain this behavior as a result of interplay between the sensing and adaptation modules of the signaling network.

Membrane-Mediated Interactions Between Protein Inclusions

Integral or peripheral membrane proteins, or protein oligomers often get close to each other on cell membranes and carry out biological tasks in a collective manner. In addition to electrostatic and van der Waals interactions, those proteins also experience membrane-mediated interactions, which may be necessary for their functionality. The membrane-mediated interactions originate from perturbation of lipid membranes by the presence of protein inclusions, and have been the subject of intensive research in membrane biophysics. Here we review both theoretical and numerical studies of such interactions for membrane proteins and for nanoparticles bound to lipid membranes.

Effect of receptor clustering on chemotactic performance of E. coli: Sensing versus adaptation

We show how the competition between sensing and adaptation can result in a performance peak in Escherichia coli chemotaxis using extensive numerical simulations in a detailed theoretical model. Receptor clustering amplifies the input signal coming from ligand binding which enhances chemotactic efficiency. But large clusters also induce large fluctuations in total activity since the number of clusters goes down. The activity and hence the run-tumble motility now gets controlled by methylation levels which are part of adaptation module rather than ligand binding. This reduces chemotactic efficiency.

Symmetry of membrane protein polyhedra with heterogeneous protein size

In experiments on membrane protein polyhedral nanoparticles (MPPNs) [Basta et al., Proc. Natl. Acad. Sci. USA 111, 670 (2014)PNASA60027-842410.1073/pnas.1321936111], it has been observed that membrane proteins and lipids can self-assemble into closed lipid bilayer vesicles with a polyhedral arrangement of membrane proteins. In particular, MPPNs formed from the mechanosensitive channel of small conductance (MscS) were found to have the symmetry of the snub cube-a chiral, Archimedean solid-with one MscS protein located at each one of the 24 vertices of the snub cube. It is currently unknown whether MPPNs with heterogeneous protein composition maintain a high degree of symmetry. Inspired by previous work on viral capsid symmetry, we employ here computational modeling to study the symmetry of MPPNs with heterogeneous protein size. We focus on MPPNs formed from MscS proteins, which can exist in closed or open conformational states with distinct sizes. We find that, as an increasing number of closed-state MscS proteins transitions to the open conformational state of MscS, the minimum-energy MscS arrangement in MPPNs follows a strikingly regular pattern, with the dominant MPPN symmetry always being provided by the snub cube. Our results suggest that MPPNs with heterogeneous protein size can be highly symmetric, with a well-defined polyhedral ordering of membrane proteins of different sizes.

Protein Recruitment through Indirect Mechanochemical Interactions

Some of the key proteins essential for important cellular processes are capable of recruiting other proteins from the cytosol to phospholipid membranes. The physical basis for this cooperativity of binding is, surprisingly, still unclear. Here, we suggest a general feedback mechanism that explains cooperativity through mechanochemical coupling mediated by the mechanical properties of phospholipid membranes. Our theory predicts that protein recruitment, and therefore also protein pattern formation, involves membrane deformation and is strongly affected by membrane composition.

Conformational switching of chiral colloidal rafts regulates raft-raft attractions and repulsions

Membrane-mediated particle interactions depend both on the properties of the particles themselves and the membrane environment in which they are suspended. Experiments have shown that chiral rod-like inclusions dissolved in a colloidal membrane of opposite handedness assemble into colloidal rafts, which are finite-sized reconfigurable droplets consisting of a large but precisely defined number of rods. We systematically tune the chirality of the background membrane and find that, in the achiral limit, colloidal rafts acquire complex structural properties and interactions. In particular, rafts can switch between 2 chiral states of opposite handedness, which alters the nature of the membrane-mediated raft-raft interactions. Rafts with the same chirality have long-ranged repulsions, while those with opposite chirality acquire attractions with a well-defined minimum. Both attractive and repulsive interactions are qualitatively explained by a continuum model that accounts for the coupling between the membrane thickness and the local tilt of the constituent rods. These switchable interactions enable assembly of colloidal rafts into intricate higher-order architectures, including stable tetrameric clusters and "ionic crystallites" of counter-twisting domains organized on a binary square lattice. Furthermore, the properties of individual rafts, such as their sizes, are controlled by their complexation with other rafts. The emergence of these complex behaviors can be rationalized purely in terms of generic couplings between compositional and orientational order of fluids of rod-like elements. Thus, the uncovered principles might have relevance for conventional lipid bilayers, in which the assembly of higher-order structures is also mediated by complex membrane-mediated interactions.

A Multi-Scale Approach to Membrane Remodeling Processes

We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.

Supramolecular organization of membrane proteins with anisotropic hydrophobic thickness

Experiments have revealed that membrane proteins often self-assemble into locally ordered clusters. Such membrane protein lattices can play key roles in the functional organization of cell membranes. Membrane protein organization can be driven, at least in part, by bilayer-mediated elastic interactions between membrane proteins. For membrane proteins with anisotropic hydrophobic thickness, bilayer-mediated protein interactions are inherently directional. Here we establish general relations between anisotropy in membrane protein hydrophobic thickness and supramolecular membrane protein organization. We show that protein symmetry is distinctively reflected in the energy landscape of bilayer-mediated protein interactions, favoring characteristic lattice architectures of membrane protein clusters. We find that, in the presence of thermal fluctuations, anisotropy in protein hydrophobic thickness can induce membrane proteins to form mesh-like structures dividing the membrane into compartments. Our results help to elucidate the physical principles and mechanisms underlying the functional organization of cell membranes.

Membrane Curvature and the Tol-Pal Complex Determine Polar Localization of the Chemoreceptor Tar in Escherichia coli

Chemoreceptors are localized at the cell poles of Escherichia coli and other rod-shaped bacteria. Over the years, different mechanisms have been put forward to explain this polar localization, including stochastic clustering, membrane curvature-driven localization, interactions with the Tol-Pal complex, and nucleoid exclusion. To evaluate these mechanisms, we monitored the cellular localization of the aspartate chemoreceptor Tar in different deletion mutants. We did not find any indication for either stochastic cluster formation or nucleoid exclusion. However, the presence of a functional Tol-Pal complex appeared to be essential to retain Tar at the cell poles. Interestingly, Tar still accumulated at midcell in tol and in pal deletion mutants. In these mutants, the protein appears to gather at the base of division septa, a region characterized by strong membrane curvature. Chemoreceptors, like Tar, form trimers of dimers that bend the cell membrane due to a rigid tripod structure. The curvature approaches the curvature of the cell membrane generated during cell division, and localization of chemoreceptor tripods at curved membrane areas is therefore energetically favorable, as it lowers membrane tension. Indeed, when we introduced mutations in Tar that abolish the rigid tripod structure, the protein was no longer able to accumulate at midcell or the cell poles. These findings favor a model where chemoreceptor localization in E. coli is driven by strong membrane curvature and association with the Tol-Pal complex.IMPORTANCE Bacteria have exquisite mechanisms to sense and adapt to the environment they live in. One such mechanism involves the chemotaxis signal transduction pathway, in which chemoreceptors specifically bind certain attracting or repelling molecules and transduce the signals to the cell. In different rod-shaped bacteria, these chemoreceptors localize specifically to cell poles. Here, we examined the polar localization of the aspartate chemoreceptor Tar in E. coli and found that membrane curvature at cell division sites and the Tol-Pal protein complex localize Tar at cell division sites, the future cell poles. This study shows how membrane curvature can guide localization of proteins in a cell.

Clustering on Membranes: Fluctuations and More

Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocytosis. Attractive forces that originate in perturbations of the membrane's physical properties contribute to this clustering, in addition to direct protein-protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to membrane-mediated clustering. Additional attractive forces that arise from protein-induced perturbation of a membrane's fluctuations are also described. This review aims to provide a survey of the current understanding of membrane-mediated clustering and how this supports precise biological functions.

Stimulus sensing and signal processing in bacterial chemotaxis

Motile bacteria use chemotaxis to migrate towards environments that are favorable for growth and survival. The signaling pathway that mediates this behavior is largely conserved among prokaryotes, with Escherichia coli chemotaxis system being one of the simplest and the best studied. At the core of this pathway are the arrays of clustered chemoreceptors that detect, amplify and integrate various stimuli. Recent work provided deeper understanding of spatial organization and signal processing by these clusters and uncovered the variety of sensory mechanisms used to detect environmental stimuli. Moreover, studies of bacteria with different lifestyles have led to new insights into the diversity and evolutionary conservation of the chemotaxis pathway, as well as the physiological relevance of chemotactic behavior in different environments.

Transmembrane region of bacterial chemoreceptor is capable of promoting protein clustering

Many membrane proteins are known to form higher-order oligomers, but the degree to which membrane regions could facilitate protein complex assembly remains largely unclear. Clusters of chemotaxis receptors are among the most prominent structures in the bacterial cell membrane, and they play important functions in processing of chemotactic signals. Although much work has been done to elucidate mechanisms of cluster formation, it almost exclusively focused on cytoplasmic interactions among receptors and other chemotaxis proteins, whereas involvement of membrane-mediated interactions was only hypothesized. Here we used imaging of constructs composed of only a fluorescent protein and the TM helices of Tar to demonstrate that interactions between the lipid bilayer and transmembrane (TM) helices of Escherichia coli chemoreceptors alone are sufficient to mediate clustering. We found that the ability to cluster depends on the sequence or length of the TM helices, implying that certain conformations of these helices facilitate clustering, whereas others do not. Notably, observed sequence specificity was apparently consistent with differences in clustering between native E. coli receptors, with the TM sequence of better-clustering high-abundance receptors being more efficient in promoting membrane-mediated complex formation. These results indicate that being more than just membrane anchors, TM helices could play an important role in the clustering and organization of membrane proteins in bacteria.

Physical model of protein cluster positioning in growing bacteria

Chemotaxic receptors in bacteria form clusters at cell poles and also laterally, and this clustering plays an important role in signal transduction. These clusters were found to be periodically arranged on the surface of the bacterium Escherichia coli, independent of any known positioning mechanism. In this work we extend a model based on diffusion and aggregation to more realistic geometries and present a means based on "bursty" protein production to distinguish spontaneous positioning from an independently existing positioning mechanism. We also consider the case of isotropic cellular growth and characterize the degree of order arising spontaneously. Our model could also be relevant for other examples of periodically positioned protein clusters in bacteria.

Origins of chemoreceptor curvature sorting in Escherichia coli

Bacterial chemoreceptors organize into large clusters at the cell poles. Despite a wealth of structural and biochemical information on the system's components, it is not clear how chemoreceptor clusters are reliably targeted to the cell pole. Here, we quantify the curvature-dependent localization of chemoreceptors in live cells by artificially deforming growing cells of Escherichia coli in curved agar microchambers, and find that chemoreceptor cluster localization is highly sensitive to membrane curvature. Through analysis of multiple mutants, we conclude that curvature sensitivity is intrinsic to chemoreceptor trimers-of-dimers, and results from conformational entropy within the trimer-of-dimers geometry. We use the principles of the conformational entropy model to engineer curvature sensitivity into a series of multi-component synthetic protein complexes. When expressed in E. coli, the synthetic complexes form large polar clusters, and a complex with inverted geometry avoids the cell poles. This demonstrates the successful rational design of both polar and anti-polar clustering, and provides a synthetic platform on which to build new systems.

Symmetry and Size of Membrane Protein Polyhedral Nanoparticles

In recent experiments [T. Basta et al., Proc. Natl. Acad. Sci. U.S.A. 111, 670 (2014)] lipids and membrane proteins were observed to self-assemble into membrane protein polyhedral nanoparticles (MPPNs) with a well-defined polyhedral protein arrangement and characteristic size. We develop a model of MPPN self-assembly in which the preferred symmetry and size of MPPNs emerge from the interplay of protein-induced lipid bilayer deformations, topological defects in protein packing, and thermal effects. With all model parameters determined directly from experiments, our model correctly predicts the observed symmetry and size of MPPNs. Our model suggests how key lipid and protein properties can be modified to produce a range of MPPN symmetries and sizes in experiments.

On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli

Bacterial mechanosensitive channels protect cells from structural damage during hypoosmotic shock. MscS, MscL and MscK are the most abundant channels in E. coli and arguably the most important ones in osmoprotection. By combining physiological assays with quantitative photo-activated localization microscopy (qPALM), we find an almost linear relationship between channel abundance and cell survival. A minimum of 100 MscL (or MscS) channels is needed for protection when a single type of channel is expressed. Under native-like conditions MscL, MscS as well as MscK distribute homogeneously over the cytoplasmic membrane and the lateral diffusion of the channels is in accordance with their relative protein mass. However, we observe cluster formation and a reduced mobility of MscL when the majority of the subunits of the pentameric channel contain the fluorescent mEos3.2 protein. These data provide new insights into the quantitative biology of mechanosensitive channels and emphasizes the need for care in analysing protein complexes even when the fluorescent tag has been optimized for monomeric behaviour.

Physics of Intracellular Organization in Bacteria

With the realization that bacteria achieve exquisite levels of spatiotemporal organization has come the challenge of discovering the underlying mechanisms. In this review, we describe three classes of such mechanisms, each of which has physical origins: the use of landmarks, the creation of higher-order structures that enable geometric sensing, and the emergence of length scales from systems of chemical reactions coupled to diffusion. We then examine the diversity of geometric cues that exist even in cells with relatively simple geometries, and end by discussing both new technologies that could drive further discovery and the implications of our current knowledge for the behavior, fitness, and evolution of bacteria. The organizational strategies described here are employed in a wide variety of systems and in species across all kingdoms of life; in many ways they provide a general blueprint for organizing the building blocks of life.

Bilayer-thickness-mediated interactions between integral membrane proteins

Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield energetically favorable bilayer-mediated interactions between integral membrane proteins, and large-scale organization of integral membrane proteins into protein clusters in cell membranes. Within the continuum elasticity theory of membranes, the energy cost of protein-induced bilayer thickness deformations can be captured by considering compression and expansion of the bilayer hydrophobic core, membrane tension, and bilayer bending, resulting in biharmonic equilibrium equations describing the shape of lipid bilayers for a given set of bilayer-protein boundary conditions. Here we develop a combined analytic and numerical methodology for the solution of the equilibrium elastic equations associated with protein-induced lipid bilayer deformations. Our methodology allows accurate prediction of thickness-mediated protein interactions for arbitrary protein symmetries at arbitrary protein separations and relative orientations. We provide exact analytic solutions for cylindrical integral membrane proteins with constant and varying hydrophobic thickness, and develop perturbative analytic solutions for noncylindrical protein shapes. We complement these analytic solutions, and assess their accuracy, by developing both finite element and finite difference numerical solution schemes. We provide error estimates of our numerical solution schemes and systematically assess their convergence properties. Taken together, the work presented here puts into place an analytic and numerical framework which allows calculation of bilayer-mediated elastic interactions between integral membrane proteins for the complicated protein shapes suggested by structural biology and at the small protein separations most relevant for the crowded membrane environments provided by living cells.

Architecture and Function of Mechanosensitive Membrane Protein Lattices

Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular organization and collective function of membrane proteins remain largely unknown. Here we show that bilayer-mediated elastic interactions between membrane proteins can yield regular and distinctive lattice architectures of protein clusters, and may provide a link between lattice architecture and lattice function. Using the mechanosensitive channel of large conductance (MscL) as a model system, we obtain relations between the shape of MscL and the supramolecular architecture of MscL lattices. We predict that the tetrameric and pentameric MscL symmetries observed in previous structural studies yield distinct lattice architectures of MscL clusters and that, in turn, these distinct MscL lattice architectures yield distinct lattice activation barriers. Our results suggest general physical mechanisms linking protein symmetry, the lattice architecture of membrane protein clusters, and the collective function of membrane protein lattices.

Protein Connectivity in Chemotaxis Receptor Complexes

The chemotaxis sensory system allows bacteria such as Escherichia coli to swim towards nutrients and away from repellents. The underlying pathway is remarkably sensitive in detecting chemical gradients over a wide range of ambient concentrations. Interactions among receptors, which are predominantly clustered at the cell poles, are crucial to this sensitivity. Although it has been suggested that the kinase CheA and the adapter protein CheW are integral for receptor connectivity, the exact coupling mechanism remains unclear. Here, we present a statistical-mechanics approach to model the receptor linkage mechanism itself, building on nanodisc and electron cryotomography experiments. Specifically, we investigate how the sensing behavior of mixed receptor clusters is affected by variations in the expression levels of CheA and CheW at a constant receptor density in the membrane. Our model compares favorably with dose-response curves from in vivo Förster resonance energy transfer (FRET) measurements, demonstrating that the receptor-methylation level has only minor effects on receptor cooperativity. Importantly, our model provides an explanation for the non-intuitive conclusion that the receptor cooperativity decreases with increasing levels of CheA, a core signaling protein associated with the receptors, whereas the receptor cooperativity increases with increasing levels of CheW, a key adapter protein. Finally, we propose an evolutionary advantage as explanation for the recently suggested CheW-only linker structures.

Receptor clusters of the bacterial chemotaxis sensory system act as antennae to amplify tiny changes in concentrations in the chemical environment of the cell, ultimately steering the cell towards nutrients and away from toxins. Despite bacterial chemotaxis being the most widely studied sensory pathway, the exact architecture of the receptor clusters remains speculative, with understanding suffering from a number of paradoxical observations. To address these issues with respect to the protein arrangement in the linkers connecting receptors, we present a statistical-mechanics model that combines insights from electron cryotomography on the linker architecture with results from fluorescence imaging of signaling in living cells. Although the signaling data for different expression levels of key molecular components in the linkers seems contradictory at first, our model reconciles these predictions with structural and biochemical data. Finally, we provide an evolutionary explanation for the observation that some of the incorporated linkers do not seem to transmit signals from the receptors.

Tubulation by amphiphysin requires concentration-dependent switching from wedging to scaffolding

BAR proteins are involved in a variety of membrane remodeling events but how they can mold membranes into different shapes remains poorly understood. Using electron paramagnetic resonance, we find that vesicle binding of the N-BAR protein amphiphysin is predominantly mediated by the shallow insertion of amphipathic N-terminal helices. In contrast, the interaction with tubes involves deeply inserted N-terminal helices together with the concave surface of the BAR domain, which acts as a scaffold. Combined with the observed concentration dependence of tubulation and BAR domain scaffolding, the data indicate that initial membrane deformations and vesicle binding are mediated by insertion of amphipathic helical wedges, while tubulation requires high protein densities at which oligomeric BAR domain scaffolds form. In addition, we identify a pocket of residues on the concave surface of the BAR domain that insert deeply into tube membrane. Interestingly, this pocket harbors a number of disease mutants in the homologous amphiphysin 2.