Rates of membrane-associated reactions: reduction of dimensionality revisited

Membrane localization accelerates association under conditions relevant to cellular signaling

Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association should be faster in the cytosol because membrane diffusion is slow. Here, we directly compare an identical association reaction, the binding of complementary DNA strands, in solution and on supported membranes. The measured rate constants show that for a 10-µm-radius spherical cell, association is 22- to 33-fold faster at the membrane than in the cytoplasm. The kinetic advantage depends on cell size and is essentially negligible for typical ~1 µm prokaryotic cells. The rate enhancement is attributable to a combination of higher encounter rates in two dimensions and a higher reaction probability per encounter.

The membrane surface as a platform that organizes cellular and biochemical processes

Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

A GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was conducted to elucidate binding mechanisms of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB). GA-mD-VcMD is a generalized ensemble method that produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions accompanied with stable maintenance of the fragile cell-membrane structure. All molecular components (bosentan, hETB, membrane, and solvent) were represented with an all-atom model. Then sampling was conducted from conformations where bosentan was distant from the binding site in the hETB binding pocket. The deepest basin in the resultant free-energy landscape was assigned to native-like complex conformation. The following binding mechanism was inferred. First, bosentan fluctuating randomly in solution is captured using a tip region of the flexible N-terminal tail of hETB via nonspecific attractive interactions (fly casting). Bosentan then slides occasionally from the tip to the root of the N-terminal tail (ligand–sliding). During this sliding, bosentan passes the gate of the binding pocket from outside to inside of the pocket with an accompanying rapid reduction of the molecular orientational variety of bosentan (orientational selection). Last, in the pocket, ligand–receptor attractive native contacts are formed. Eventually, the native-like complex is completed. The bosentan-captured conformations by the tip-region and root-region of the N-terminal tail correspond to two basins in the free-energy landscape. The ligand-sliding corresponds to overcoming of a free-energy barrier between the basins.

Exploring the kinetic selectivity of drugs targeting the β1 -adrenoceptor

In this study, we report the β1 -adrenoceptor binding kinetics of several clinically relevant β1/2 -adrenoceptor (β1/2 AR) agonists and antagonists. [3 H]-DHA was used to label CHO-β1 AR for binding studies. The kinetics of ligand binding was assessed using a competition association binding method. Ligand physicochemical properties, including logD7.4 and the immobilized artificial membrane partition coefficient (KIAM ), were assessed using column-based methods. Protein Data Bank (PDB) structures and hydrophobic and electrostatic surface maps were constructed in PyMOL. We demonstrate that the hydrophobic properties of a molecule directly affect its kinetic association rate (kon ) and affinity for the β1 AR. In contrast to our findings at the β2 -adrenoceptor, KIAM , reflecting both hydrophobic and electrostatic interactions of the drug with the charged surface of biological membranes, was no better predictor than simple hydrophobicity measurements such as clogP or logD7.4 , at predicting association rate. Bisoprolol proved kinetically selective for the β1 AR subtype, dissociating 50 times slower and partly explaining its higher measured affinity for the β1 AR. We speculate that the association of positively charged ligands at the β1 AR is curtailed somewhat by its predominantly neutral/positive charged extracellular surface. Consequently, hydrophobic interactions in the ligand-binding pocket dominate the kinetics of ligand binding. In comparison at the β2 AR, a combination of hydrophobicity and negative charge attracts basic, positively charged ligands to the receptor's surface promoting the kinetics of ligand binding. Additionally, we reveal the potential role kinetics plays in the on-target and off-target pharmacology of clinically used β-blockers.

Phosphoinositide-binding activity of Smad2 is essential for its function in TGF-β signaling

As a central player in the canonical TGF-β signaling pathway, Smad2 transmits the activation of TGF-β receptors at the plasma membrane (PM) to transcriptional regulation in the nucleus. Although it has been well established that binding of TGF-β to its receptors leads to the recruitment and activation of Smad2, the spatiotemporal mechanism by which Smad2 is recruited to the activated TGF-β receptor complex and activated is not fully understood. Here we show that Smad2 selectively and tightly binds phosphatidylinositol-4,5-bisphosphate (PI(4,5)P₂) in the PM. The PI(4,5)P₂-binding site is located in the MH2 domain that is involved in interaction with the TGF-β receptor I that transduces TGF-β-receptor binding to downstream signaling proteins. Quantitative optical imaging analyses show that PM recruitment of Smad2 is triggered by its interaction with PI(4,5)P₂ that is locally enriched near the activated TGF-β receptor complex, leading to its binding to the TGF-β receptor I. The PI(4,5)P₂-binding activity of Smad2 is essential for the TGF-β-stimulated phosphorylation, nuclear transport, and transcriptional activity of Smad2. Structural comparison of all Smad MH2 domains suggests that membrane lipids may also interact with other Smad proteins and regulate their function in diverse TGF-β-mediated biological processes.

Enterovirus Replication Organelles and Inhibitors of Their Formation

Enteroviral replication reorganizes the cellular membrane. Upon infection, viral proteins and hijacked host factors generate unique structures called replication organelles (ROs) to replicate their viral genomes. ROs promote efficient viral genome replication, coordinate the steps of the viral replication cycle, and protect viral RNA from host immune responses. More recent researches have focused on the ultrastructure structures, formation mechanism, and functions in the virus life cycle of ROs. Dynamic model of enterovirus ROs structure is proposed, and the secretory pathway, the autophagy pathway, and lipid metabolism are found to be associated in the formation of ROs. With deeper understanding of ROs, some compounds have been found to show inhibitory effects on viral replication by targeting key proteins in the process of ROs formation. Here, we review the recent findings concerning the role, morphology, biogenesis, formation mechanism, and inhibitors of enterovirus ROs.

Modified nucleotides may have enhanced early RNA catalysis

The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication.

Stability Analysis of a Bulk-Surface Reaction Model for Membrane Protein Clustering

Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on the surface of the PM plays an important role in governing their heterogeneous surface distribution. However, the stability behavior of the surface distribution of protein aggregates remains poorly understood. Therefore, understanding the spatial patterns that can emerge on the PM solely through protein-protein interaction, lateral diffusion, and feedback is an important step toward a complete description of the mechanisms behind protein clustering on the cell surface. In this work, we investigate the pattern formation of a reaction-diffusion model that describes the dynamics of a system of ligand-receptor complexes. The purely diffusive ligand in the cytosol can bind receptors in the PM and the resultant ligand-receptor complexes not only diffuse laterally but can also form clusters resulting in different oligomers. Finally, the largest oligomers recruit ligands from the cytosol using positive feedback. From a methodological viewpoint, we provide theoretical estimates for diffusion-driven instabilities of the protein aggregates based on the Turing mechanism. Our main result is a threshold phenomenon, in which a sufficiently high recruitment of ligands promotes the input of new monomeric components and consequently drives the formation of a single-patch spatially heterogeneous steady state.

Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate

A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al., 2018, Nature 558:564-568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin ("prebiotic soup"). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.

Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors?

The ligand-binding sites of many G protein-coupled receptors (GPCRs) are situated around and deeply embedded within the central pocket formed by their seven transmembrane-spanning α-helical domains. Generally, these binding sites are assumed accessible to endogenous ligands from the aqueous phase. Recent advances in the structural biology of GPCRs, along with biophysical and computational studies, suggest that amphiphilic and lipophilic molecules may gain access to these receptors by first partitioning into the membrane and then reaching the binding site via lateral diffusion through the lipid bilayer. In addition, several crystal structures of class A and class B GPCRs bound to their ligands offer unprecedented details on the existence of lipid-facing allosteric binding sites outside the transmembrane helices that can only be reached via lipid pathways. The highly organized structure of the lipid bilayer may direct lipophilic or amphiphilic drugs to a specific depth within the bilayer, changing local concentration of the drug near the binding site and affecting its binding kinetics. Additionally, the constraints of the lipid bilayer, including its composition and biophysical properties, may play a critical role in "pre-organizing" ligand molecules in an optimal orientation and conformation to facilitate receptor binding. Despite its clear involvement in molecular recognition processes, the critical role of the membrane in binding ligands to lipid-exposed transmembrane binding sites remains poorly understood and warrants comprehensive investigation. Understanding the mechanistic basis of the structure-membrane interaction relationship of drugs will not only provide useful insights about receptor binding kinetics but will also enhance our ability to take advantage of the apparent membrane contributions when designing drugs that target transmembrane proteins with improved efficacy and safety. In this minireview, we summarize recent structural and computational studies on membrane contributions to binding processes, elucidating both lipid pathways of ligand access and binding mechanisms for several orthosteric and allosteric ligands of class A and class B GPCRs.

Membrane properties that shape the evolution of membrane enzymes

Spectacular recent progress in structural biology has led to determination of the structures of many integral membrane enzymes that catalyze reactions in which at least one substrate also is membrane bound. A pattern of results seems to be emerging in which the active site chemistry of these enzymes is usually found to be analogous to what is observed for water soluble enzymes catalyzing the same reaction types. However, in light of the chemical, structural, and physical complexity of cellular membranes plus the presence of transmembrane gradients and potentials, these enzymes may be subject to membrane-specific regulatory mechanisms that are only now beginning to be uncovered. We review the membrane-specific environmental traits that shape the evolution of membrane-embedded biocatalysts.

Cytosolic proteins can exploit membrane localization to trigger functional assembly

Cell division, endocytosis, and viral budding would not function without the localization and assembly of protein complexes on membranes. What is poorly appreciated, however, is that by localizing to membranes, proteins search in a reduced space that effectively drives up concentration. Here we derive an accurate and practical analytical theory to quantify the significance of this dimensionality reduction in regulating protein assembly on membranes. We define a simple metric, an effective equilibrium constant, that allows for quantitative comparison of protein-protein interactions with and without membrane present. To test the importance of membrane localization for driving protein assembly, we collected the protein-protein and protein-lipid affinities, protein and lipid concentrations, and volume-to-surface-area ratios for 46 interactions between 37 membrane-targeting proteins in human and yeast cells. We find that many of the protein-protein interactions between pairs of proteins involved in clathrin-mediated endocytosis in human and yeast cells can experience enormous increases in effective protein-protein affinity (10–1000 fold) due to membrane localization. Localization of binding partners thus triggers robust protein complexation, suggesting that it can play an important role in controlling the timing of endocytic protein coat formation. Our analysis shows that several other proteins involved in membrane remodeling at various organelles have similar potential to exploit localization. The theory highlights the master role of phosphoinositide lipid concentration, the volume-to-surface-area ratio, and the ratio of 3D to 2D equilibrium constants in triggering (or preventing) constitutive assembly on membranes. Our simple model provides a novel quantitative framework for interpreting or designing in vitro experiments of protein complexation influenced by membrane binding.

In a multitude of cellular processes, including cell division and endocytosis, proteins must bind to one another to form large multi-protein complexes. To initiate the formation of these critical multi-protein assemblies at the right time and the right place, the constituent proteins must be present at sufficient concentrations. We show here that membrane localization offers a powerful way of controlling protein concentrations by reducing the dimensionality of the protein’s search space. We present a simple and practical analytical theory that determines the significance of membrane localization for triggering protein-protein interactions. We show that protein binding partners will often form substantially more complexes when both partners can localize to surfaces, and thus localization can regulate the timing of multi-protein assembly. We collect in vitro binding data and cellular concentrations of proteins and lipids involved in pathways including clathrin-mediated endocytosis to demonstrate how cellular proteins could exploit membrane localization to regulate assembly.

Interaction of semiochemicals with model lipid membranes: A biophysical approach

Unravelling the chemical language of insects has been the subject of intense research in the field of chemical ecology for the past five decades. Insect communication is mainly based on chemosensation due to the small body size of insects, which limits their ability to produce or perceive auditory and visual signals, especially over large distances. Chemicals involved in insect communication are called semiochemicals. These volatiles and semivolatiles compounds allow to Insects to find a mate, besides the oviposition site in reproduction and food sources. Actually, insect olfaction mechanism is subject to study, but systematic analyses of the role of neural membranes are scarce. In the present work we evaluated the interactions of α-pinene, benzaldehyde, eugenol, and grandlure, among others, with a lipid membrane model using surface pressure experiments and Monte Carlo computational analysis. This allowed us to propose a plausible membranotropic mechanism of interaction between semiochemicals and insect neural membrane.

Hetero-multivalent binding of cholera toxin subunit B with glycolipid mixtures

GM₁ has generally been considered as the major receptor that binds to cholera toxin subunit B (CTB) due to its low dissociation constant. However, using a unique nanocube sensor technology, we have shown that CTB can also bind to other glycolipid receptors, fucosyl-GM₁ and GD₁b. Additionally, we have demonstrated that GM₂ can contribute to CTB binding if present in a glycolipid mixture with a strongly binding receptor (GM₁/fucosyl-GM₁/GD₁b). This hetero-multivalent binding result was unintuitive because the interaction between CTB and pure GM₂ is negligible. We hypothesized that the reduced dimensionality of CTB-GM₂ binding events is a major cause of the observed CTB binding enhancement. Once CTB has attached to a strong receptor, subsequent binding events are confined to a 2D membrane surface. Therefore, even a weak GM₂ receptor could now participate in second or higher binding events because its surface reaction rate can be up to 10⁴ times higher than the bulk reaction rate. To test this hypothesis, we altered the surface reaction rate by modulating the fluidity and heterogeneity of the model membrane. Decreasing membrane fluidity reduced the binding cooperativity between GM₂ and a strong receptor. Our findings indicated a new protein-receptor binding assay, that can mimic complex cell membrane environment more accurately, is required to explore the inherent hetero-multivalency of the cell membrane. We have thus developed a new membrane perturbation protocol to efficiently screen receptor candidates involved in hetero-multivalent protein binding.

Interactions between β2-Adrenoceptor Ligands and Membrane: Atomic-Level Insights from Magic-Angle Spinning NMR

To understand the relationship between structural properties of the β2-adrenoceptor ligands and their interactions with membranes, we have investigated the location and distribution of five β2 agonists with distinct clinical durations and onsets of action (indacaterol, two indacaterol analogues, salmeterol and formoterol) in monounsaturated model membranes using magic angle spinning NMR to measure these interactions through both ¹H nuclear Overhauser enhancement (NOE) and paramagnetic relaxation enhancement (PRE) techniques. The hydrophilic aromatic groups of all five β2 agonists show maximum distribution in the lipid/water interface, but distinct location and dynamic behavior were observed for the lipophilic aromatic rings. Our study elucidates at atomic level that the hydrophobicity and substitution geometry of lipophilic groups play important roles in compound-lipid interactions.

Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane

Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.

Peripheral membrane associations of matrix metalloproteinases

Water soluble matrix metalloproteinases (MMPs) have been regarded as diffusing freely in the extracellular matrix. Yet multiple MMPs are also observed at cell surfaces. Their membrane-proximal activities include sheddase activities, collagenolysis, bacterial killing, and intracellular trafficking reaching as far as the nucleus. The catalytic domains of MMP-7 and MMP-12 bind bilayers peripherally, each in two different orientations, by presenting positive charges and a few hydrophobic groups to the surface. Related peripheral membrane associations are predicted for other soluble MMPs. The peripheral membrane associations may support pericellular proteolysis and endocytosis. The isolated soluble domains of MT1-MMP can also associate with membranes. NMR assays suggest transient association of the hemopexin-like domains of MT1-MMP and MMP-12 with lipid bilayers. Peripheral association of soluble MMP domains with bilayers or heparin sulfate proteoglycans probably concentrates them near the membrane. This could increase the probability of forming complexes with membrane-associated proteins, such as those targeted for proteolysis. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.

Lipid Tales of Viral Replication and Transmission

Positive-strand RNA viruses are the largest group of RNA viruses on Earth and cellular membranes are critical for all aspects of their life cycle, from entry and replication to exit. In particular, membranes serve as platforms for replication and as carriers to transmit these viruses to other cells, the latter either as an envelope surrounding a single virus or as the vesicle containing a population of viruses. Notably, many animal and human viruses appear to induce and exploit phosphatidylinositol 4-phosphate/cholesterol-enriched membranes for replication, whereas many plant and insect-vectored animal viruses utilize phosphatidylethanolamine/cholesterol-enriched membranes for the same purpose; and phosphatidylserine-enriched membrane carriers are widely used by both single and populations of viruses for transmission. Here I discuss the implications for viral pathogenesis and therapeutic development of this remarkable convergence on specific membrane lipid blueprints for replication and transmission.

Reaction-diffusion basis of retroviral infectivity

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env₃) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env₃ molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env₃ diffuses comparably to Gag-absent Env₃ Initial immobility of Env₃ is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env₃ diffusion, and permits Env₃ clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Application of Peak Intensity Analysis to Measurements of Protein Binding to Lipid Vesicles and Erythrocytes Using Fluorescence Correlation Spectroscopy: Dependence on Particle Size

Fluorescence correlation spectroscopy (FCS) is a sensitive analytical tool for investigation of processes accompanied by changes in the mobility of molecules and complexes. In the present work, peak intensity analysis (PIA) in combination with the solution stirring using FCS setup was applied to explore the interaction between fluorescently labeled protein ligands and corresponding receptors located on membranes. In the system composed of biotinylated liposomes and fluorescently labeled streptavidin as a ligand, PIA allowed us to determine the optimum receptor concentration and demonstrate the essential dependence of the binding efficacy on the length of the linker between the biotin group and the polar head group of the lipid. The binding was dependent on the size of liposomes which was varied by lipid extrusion through filters of different pore diameters. The sensitivity of the method was higher with the liposomes of larger sizes. The PIA approach can be applied not only to liposomes but also to relatively large objects, e.g., erythrocytes or Sepharose beads derivatized with lactose as a receptor for the binding of viscumin and ricin.

Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding

Ligand binding to membrane proteins may be significantly influenced by the interaction of ligands with the membrane. In particular, the microscopic ligand concentration within the membrane surface solvation layer may exceed that in bulk solvent, resulting in overestimation of the intrinsic protein-ligand binding contribution to the apparent/measured affinity. Using published binding data for a set of small molecules with the β2 adrenergic receptor, we demonstrate that deconvolution of membrane and protein binding contributions allows for improved structure-activity relationship analysis and structure-based drug design. Molecular dynamics simulations of ligand bound membrane protein complexes were used to validate binding poses, allowing analysis of key interactions and binding site solvation to develop structure-activity relationships of β2 ligand binding. The resulting relationships are consistent with intrinsic binding affinity (corrected for membrane interaction). The successful structure-based design of ligands targeting membrane proteins may require an assessment of membrane affinity to uncouple protein binding from membrane interactions.

Modeling bispecific monoclonal antibody interaction with two cell membrane targets indicates the importance of surface diffusion

We have developed a mathematical framework for describing a bispecific monoclonal antibody interaction with two independent membrane-bound targets that are expressed on the same cell surface. The bispecific antibody in solution binds either of the two targets first, and then cross-links with the second one while on the cell surface, subject to rate-limiting lateral diffusion step within the lifetime of the monovalently engaged antibody-antigen complex. At experimental densities, only a small fraction of the free targets is expected to lie within the reach of the antibody binding sites at any time. Using ordinary differential equation and Monte Carlo simulation-based models, we validated this approach against an independently published anti-CD4/CD70 DuetMab experimental data set. As a result of dimensional reduction, the cell surface reaction is expected to be so rapid that, in agreement with the experimental data, no monovalently bound bispecific antibody binary complexes accumulate until cross-linking is complete. The dissociation of the bispecific antibody from the ternary cross-linked complex is expected to be significantly slower than that from either of the monovalently bound variants. We estimate that the effective affinity of the bivalently bound bispecific antibody is enhanced for about 4 orders of magnitude over that of the monovalently bound species. This avidity enhancement allows for the highly specific binding of anti-CD4/CD70 DuetMab to the cells that are positive for both target antigens over those that express only one or the other We suggest that the lateral diffusion of target antigens in the cell membrane also plays a key role in the avidity effect of natural antibodies and other bivalent ligands in their interactions with their respective cell surface receptors.

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.

Juxtacrine signaling is inherently noisy

Juxtacrine signaling is an important class of signaling systems that plays a crucial role in various developmental processes ranging from coordination of differentiation between neighboring cells to guiding axon growth during neurogenesis. Such signaling systems rely on the interaction between receptors on one cell and trans-membrane ligands on the membrane of a neighboring cell. Like other signaling systems, the ability of signal-receiving cells to accurately determine the concentration of ligands, is affected by stochastic diffusion processes. However, it is not clear how restriction of ligand movement to the two-dimensional (2D) cell membrane in juxtacrine signaling affects the accuracy of ligand sensing. In this study, we use a statistical mechanics approach, to show that long integration times, from around one second to several hours, are required to reach high-sensing accuracy (better than 10%). Surprisingly, the accuracy of sensing cannot be significantly improved, neither by increasing the number of receptors above three to five receptors per contact area, nor by increasing the contact area between cells. We show that these results impose stringent constraints on the dynamics of processes relying on juxtacrine signaling systems, such as axon guidance mediated by Ephrins and developmental patterns mediated by the Notch pathway.

On the 'micro'-pharmacodynamic and pharmacokinetic mechanisms that contribute to long-lasting drug action

INTRODUCTION

Optimal drug therapy often requires continuing high levels of target occupancy. Besides the traditional pharmacokinetic (PK) contribution thereto, drug-target interactions that comprise successive 'microscopic' steps as well as the intervention of the cell membrane and other 'micro'-anatomical structures nearby may help attaining this objective.

AREAS COVERED

This article reviews the 'micro'-pharmacodynamic (PD) and PK mechanisms that may increase a drug's residence time. Special focus is on induced-fit- and bivalent ligand binding models as well as on the ability of the plasma membrane surrounding the target to act as a repository for the drug (e.g., microkinetic model), to actively participate in the binding process (e.g., exosite model) and, along with microanatomical elements like synapses and interstitial spaces, to act on the drug's diffusion properties (reduction in dimensionality and drug-rebinding models).

EXPERT OPINION

The PK profile, as well as the target dissociation kinetics of a drug, may fail to account for its long-lasting efficiency in intact tissues and in vivo. This lacuna could potentially be alleviated by incorporating some of the enumerated 'microscopic' mechanisms and, to unveil them, dedicated experiments on sufficiently physiologically relevant biological material like cell monolayers can already be implemented early on in the lead optimization process.

The limits of chemosensation vary across dimensions

Many biological processes rely on the ability of cells to measure local ligand concentration. However, such measurements are constrained by noise arising from diffusion and the stochastic nature of receptor–ligand interactions. It is thus critical to understand how accurately, in principle, concentration measurements can be made. Previous theoretical work has mostly investigated this in 3D under the simplifying assumption of an unbounded domain of diffusion, but many biological problems involve 2D concentration measurement in bounded domains, for which diffusion behaves quite differently. Here we present a theory of the precision of chemosensation that covers bounded domains of any dimensionality. We find that the quality of chemosensation in lower dimensions is controlled by domain size, suggesting a general principle applicable to many biological systems. Applying the theory to biological problems in 2D shows that diffusion-limited signalling is an efficient mechanism on time scales consistent with behaviour.

Theoretical studies on chemosensation often invoke a model of three dimensional unbounded diffusion, but many biological problems involve two-dimensional diffusion in a bounded domain. Here Bicknell et al. present a model for chemosensation that covers bounded domains of any dimension, and apply it to biological problems in two dimensions.

Diversity and selectivity in mRNA translation on the endoplasmic reticulum

Pioneering electron microscopy studies defined two primary populations of ribosomes in eukaryotic cells: one freely dispersed through the cytoplasm and the other bound to the surface of the endoplasmic reticulum (ER). Subsequent investigations revealed a specialized function for each population, with secretory and integral membrane protein-encoding mRNAs translated on ER-bound ribosomes, and cytosolic protein synthesis was widely attributed to free ribosomes. Recent findings have challenged this view, and transcriptome-scale studies of mRNA distribution and translation have now demonstrated that ER-bound ribosomes also function in the translation of a large fraction of mRNAs that encode cytosolic proteins. These studies suggest a far more expansive role for the ER in transcriptome expression, where membrane and secretory protein synthesis represents one element of a multifaceted and dynamic contribution to post-transcriptional gene expression.

Immobilized IL-8 Triggers Phagocytosis and Dynamic Changes in Membrane Microtopology in Human Neutrophils

The interaction of leukocytes with surface bound ligands can be limited by the location of the molecules relative to the surface topology of the cell. In this report, we examine the dynamic response of neutrophils to IL-8-fractalkine chimera immobilized on bead surfaces, taking into account changes in receptor occupancy resulting from changes in surface topography. As a readout for receptor signaling, we observe the dynamics of calcium release in neutrophils following contact with the IL-8 coated surface. After a delay that depended on the initial area of contact and the surface density of IL-8, the cell began to phagocytose the IL-8 coated bead. This appeared to be a pre-requisite for release of calcium, which typically followed shortly after the initiation of phagocytosis. In separate experiments, effective kinetic coefficients for the formation of bonds between immobilized IL-8 and receptors on the cell surface were determined. Using these coefficients, we were able to estimate the number of bound receptors in the nascent contact zone. Kinetic modeling of the signaling response predicted that cell spreading and a concomitant increase in the density of occupied receptors would be required for the experimentally observed calcium dynamics. Postulating that there is an increase in receptor occupancy resulting from smoothing of the cell surface as it is stretched over the bead enabled us to obtain model predictions consistent with experimental observations. This study reveals the likely importance of membrane microtopology as a rate-limiting property and potential means of regulation of cell responses stimulated by two-dimensional surface interactions.

The proapoptotic protein tBid forms both superficially bound and membrane-inserted oligomers

Bid is a proapopotic activator protein of the Bcl-2 family that plays a pivotal role in controlling mitochondrial outer membrane permeabilization during apoptosis. Here, we characterized the interaction of fluorescently labeled truncated Bid (tBid) with a mitochondria-like supported lipid bilayer at the single-molecule level. The proteins observed at the membrane exhibited a very wide range of mobility. Confocal images of the membrane displayed both diffraction-limited Gaussian spots and horizontal streaks, corresponding to immobile and mobile tBid species, respectively. We observed 1), fast-diffusing proteins corresponding to a loosely, probably electrostatically bound state; 2), slowly diffusing proteins, likely corresponding to a superficially inserted state; and 3), fully immobilized proteins, suggesting a fully inserted state. The stoichiometry of these proteins was determined by normalizing their fluorescence intensity by the brightness of a tBid monomer, measured separately using fluorescence fluctuation techniques. Strikingly, the immobile species were found to be mainly tetramers and higher, whereas the mobile species had on average a significantly lower stoichiometry. Taken together, these results show that as soluble Bid progresses toward a membrane-inserted state, it undergoes an oligomerization process similar to that observed for Bax.

DNA-cholesterol barges as programmable membrane-exploring agents

DNA nanotechnology enables the precise construction of nanoscale devices that mimic aspects of natural biomolecular systems yet exhibit robustly programmable behavior. While many important biological processes involve dynamic interactions between components associated with phospholipid membranes, little progress has been made toward creating synthetic mimics of such interfacial systems. We report the assembly and characterization of cholesterol-labeled DNA origami "barges" capable of reversible association with and lateral diffusion on supported lipid bilayers. Using single-particle fluorescence microscopy, we show that these DNA barges rapidly and stably embed in lipid bilayers and exhibit Brownian diffusion in a manner dependent on both cholesterol labeling and bilayer composition. Tracking of individual barges rapidly generates super-resolution maps of the contiguous regions of a membrane. Addition of appropriate command oligonucleotides enables membrane-associated barges to reversibly exchange fluorescent cargo with bulk solution, dissociate from the membrane, or form oligomers within the membrane, opening up new possibilities for programmable membrane-bound molecular devices.

Enteroviruses harness the cellular endocytic machinery to remodel the host cell cholesterol landscape for effective viral replication

Cholesterol is a critical component of cellular membranes, regulating assembly and function of membrane-based protein/lipid complexes. Many RNA viruses, including enteroviruses, remodel host membranes to generate organelles with unique lipid blueprints on which they assemble replication complexes and synthesize viral RNA. Here we find that clathrin-mediated endocytosis (CME) is harnessed by enteroviruses to traffic cholesterol from the plasma membrane (PM) and extracellular medium to replication organelles, where cholesterol then regulates viral polyprotein processing and facilitates genome synthesis. When CME is disrupted, cellular cholesterol pools are instead stored in lipid droplets, cholesterol cannot be trafficked to replication organelles, and replication is inhibited. In contrast, replication is stimulated in cholesterol-elevated cells like those lacking caveolins or those from Niemann-Pick disease patients. Our findings indicate cholesterol as a critical determinant for enteroviral replication and outline roles for the endocytic machinery in both the enteroviral life cycle and host cell cholesterol homeostasis.

Microtubules accelerate the kinase activity of Aurora-B by a reduction in dimensionality

Aurora-B is the kinase subunit of the Chromosome Passenger Complex (CPC), a key regulator of mitotic progression that corrects improper kinetochore attachments and establishes the spindle midzone. Recent work has demonstrated that the CPC is a microtubule-associated protein complex and that microtubules are able to activate the CPC by contributing to Aurora-B auto-phosphorylation in trans. Aurora-B activation is thought to occur when the local concentration of Aurora-B is high, as occurs when Aurora-B is enriched at centromeres. It is not clear, however, whether distributed binding to large structures such as microtubules would increase the local concentration of Aurora-B. Here we show that microtubules accelerate the kinase activity of Aurora-B by a "reduction in dimensionality." We find that microtubules increase the kinase activity of Aurora-B toward microtubule-associated substrates while reducing the phosphorylation levels of substrates not associated to microtubules. Using the single molecule assay for microtubule-associated proteins, we show that a minimal CPC construct binds to microtubules and diffuses in a one-dimensional (1D) random walk. The binding of Aurora-B to microtubules is salt-dependent and requires the C-terminal tails of tubulin, indicating that the interaction is electrostatic. We show that the rate of Aurora-B auto-activation is faster with increasing concentrations of microtubules. Finally, we demonstrate that microtubules lose their ability to stimulate Aurora-B when their C-terminal tails are removed by proteolysis. We propose a model in which microtubules act as scaffolds for the enzymatic activity of Aurora-B. The scaffolding activity of microtubules enables rapid Aurora-B activation and efficient phosphorylation of microtubule-associated substrates.

Mathematical modelling and computational study of two-dimensional and three-dimensional dynamics of receptor-ligand interactions in signalling response mechanisms

Cell signalling processes involve receptor trafficking through highly connected networks of interacting components. The binding of surface receptors to their specific ligands is a key factor for the control and triggering of signalling pathways. But the binding process still presents many enigmas and, by analogy with surface catalytic reactions, two different mechanisms can be conceived: the first mechanism is related to the Eley-Rideal (ER) mechanism, i.e. the bulk-dissolved ligand interacts directly by pure three-dimensional (3D) diffusion with the specific surface receptor; the second mechanism is similar to the Langmuir-Hinshelwood (LH) process, i.e. 3D diffusion of the ligand to the cell surface followed by reversible ligand adsorption and subsequent two-dimensional (2D) surface diffusion to the receptor. A situation where both mechanisms simultaneously contribute to the signalling process could also occur. The aim of this paper is to perform a computational study of the behavior of the signalling response when these different mechanisms for ligand-receptor interactions are integrated into a model for signal transduction and ligand transport. To this end, partial differential equations have been used to develop spatio-temporal models that show trafficking dynamics of ligands, cell surface components, and intracellular signalling molecules through the different domains of the system. The mathematical modeling developed for these mechanisms has been applied to the study of two situations frequently found in cell systems: (a) dependence of the signal response on cell density; and (b) enhancement of the signalling response in a synaptic environment.

Phosphatidylinositol 4-kinases: hostages harnessed to build panviral replication platforms

Several RNA viruses have recently been shown to hijack members of the host phosphatidylinositol (PtdIns) 4-kinase (PI4K) family of enzymes. They use PI4K to generate membranes enriched in phosphatidylinositide 4-phosphate (PtdIns4P or PI4P) lipids, which can be used as replication platforms. Viral replication machinery is assembled on these platforms as a supramolecular complex and PtdIns4P lipids regulate viral RNA synthesis. This article highlights these recent studies on the regulation of viral RNA synthesis by PtdIns4P lipids. It explores the potential mechanisms by which PtdIns4P lipids can contribute to viral replication and discusses the therapeutic potential of developing antiviral molecules that target host PI4Ks as a form of panviral therapy.

Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions

Emerging evidence indicates that membrane lipids regulate protein networking by directly interacting with protein-interaction domains (PIDs). As a pilot study to identify and functionally annodate lipid-binding PIDs on a genomic scale, we performed experimental and computational studies of PDZ domains. Characterization of 70 PDZ domains showed that ~40% had submicromolar membrane affinity. Using a computational model built from these data, we predicted the membrane-binding properties of 2,000 PDZ domains from 20 species. The accuracy of the prediction was experimentally validated for 26 PDZ domains. We also subdivided lipid-binding PDZ domains into three classes based on the interplay between membrane- and protein-binding sites. For different classes of PDZ domains, lipid binding regulates their protein interactions by different mechanisms. Functional studies of a PDZ domain protein, rhophilin 2, suggest that all classes of lipid-binding PDZ domains serve as genuine dual-specificity modules regulating protein interactions at the membrane under physiological conditions.

The membrane environment can promote or suppress bistability in cell signaling networks

Many key biochemical reactions that mediate signal transduction in cells occur at the cell membrane, yet how the two-dimensional membrane environment influences the collective behavior of signaling networks is poorly understood. We study models of two topologically different signaling pathways that exhibit bistability, examining the effects of reduced protein mobility and increased concentration at the membrane, as well as effects due to differences in spatiotemporal correlations between the membrane environment and three-dimensional cytoplasm. The two model networks represent the distributive enzymatic modification of a protein at multiple sites and the positive feedback-mediated activation of a protein. In both cases, we find that confining proteins to a membrane-like environment can markedly alter the emergent dynamics. For the distributive protein modification network, increased concentration promotes bistability through enhanced protein-protein binding, while lower mobility and membrane-enhanced spatiotemporal correlations suppress bistability. For the positive feedback-mediated activation network, confinement to a membrane environment enhances protein activation, which can induce bistability or stabilize a monostable, active state. Importantly, the influence of the membrane environment on signaling dynamics can be qualitatively different for signaling modules with different network topologies.

Coupling exo- and endocytosis: an essential role for PIP₂ at the synapse

Chemical synapses are specialist points of contact between two neurons, where information transfer takes place. Communication occurs through the release of neurotransmitter substances from small synaptic vesicles in the presynaptic terminal, which fuse with the presynaptic plasma membrane in response to neuronal stimulation. However, as neurons in the central nervous system typically only possess ~200 vesicles, high levels of release would quickly lead to a depletion in the number of vesicles, as well as leading to an increase in the area of the presynaptic plasma membrane (and possible misalignment with postsynaptic structures). Hence, synaptic vesicle fusion is tightly coupled to a local recycling of synaptic vesicles. For a long time, however, the exact molecular mechanisms coupling fusion and subsequent recycling remained unclear. Recent work now indicates a unique role for the plasma membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP(2)), acting together with the vesicular protein synaptotagmin, in coupling these two processes. In this work, we review the evidence for such a mechanism and discuss both the possible advantages and disadvantages for vesicle recycling (and hence signal transduction) in the nervous system. This article is part of a Special Issue entitled Lipids and Vesicular Transport.

HAMLET forms annular oligomers when deposited with phospholipid monolayers

Recently, the anticancer activity of human α-lactalbumin made lethal to tumor cells (HAMLET) has been linked to its increased membrane affinity in vitro, at neutral pH, and ability to cause leakage relative to the inactive native bovine α-lactalbumin (BLA) protein. In this study, atomic force microscopy resolved membrane distortions and annular oligomers (AOs) produced by HAMLET when deposited at neutral pH on mica together with a negatively charged lipid monolayer. BLA, BAMLET (HAMLET's bovine counterpart) and membrane-binding Peptide C, corresponding to BLA residues 75-100, also form AO-like structures under these conditions but at higher subphase concentrations than HAMLET. The N-terminal Peptide A, which binds to membranes at acidic but not at neutral pH, did not form AOs. This suggests a correlation between the capacity of the proteins/peptides to integrate into the membrane at neutral pH-as observed by liposome content leakage and circular dichroism experiments-and the formation of AOs, albeit at higher concentrations. Formation of AOs, which might be important to HAMLET's tumor toxic action, appears related to the increased tendency of the protein to populate intermediately folded states compared to the native protein, the formation of which is promoted by, but not uniquely dependent on, the oleic acid molecules associated with HAMLET.

The role of long-range intermolecular interactions in discovery of new drugs

INTRODUCTION

Long-range intermolecular interactions (interactions at distances between 100 and 1000 Å) play an important role in the interaction between drugs and therapeutic targets, and design techniques based on this concept could significantly improve and accelerate new drug discovery. Understanding these long-range intermolecular interactions will also help further our understanding of the molecular mechanisms and the underlying basic biological processes.

AREAS COVERED

This article looks at the physical bases of long-range intermolecular interactions in biological systems with a brief review of the literature data to support this concept. The article also gives some examples of techniques used in drug discovery that were based on the long-range intermolecular interaction concept.

EXPERT OPINION

The electron-ion interaction potential (EIIP) and average quasivalence number (AQVN) concepts shed new light on the role of long-range intermolecular interactions in biological systems. Further research of physicochemical mechanisms underlying long-range interactions between biological molecules is necessary for a better understanding of the basic biological processes. The addition of the computer-aided design techniques based on the EIIP/AQVN concept to the research and development will lead not only to a significant reduction in cost but also to an acceleration in the development of new drugs.

Membrane catalysis of peptide-receptor binding

The membrane catalysis hypothesis states that a peptide ligand activates its target receptor after an initial interaction with the surrounding membrane. Upon membrane binding and interaction, the ligand is structured such that receptor binding and activation is encouraged. As evidence for this hypothesis, there are numerous studies concerning the conformation that peptides adopt in membrane mimetic environments. This mini-review analyzes the features of ligand peptides with an available high-resolution membrane-induced structure and a characterized membrane-binding region. At the peptide-membrane interface, both amphipathic helices and turn structures are commonly formed in peptide ligands and both hydrophobic and electrostatic interactions can be responsible for membrane binding. Apelin is the ligand to the G-protein coupled receptor (GPCR) named APJ, with various important physiological effects, which we have recently characterized both in solution and bound to anionic micelles. The structural changes that apelin undergoes when binding to micelles provide strong evidence for membrane catalysis of apelin-APJ interactions.

Cholesterol depletion mimics the effect of cytoskeletal destabilization on membrane dynamics of the serotonin1A receptor: A zFCS study

Single-point fluorescence correlation spectroscopy (FCS) of membrane-bound molecules suffers from a number of limitations leading to inaccurate estimation of diffusion parameters. To overcome such problems and with the overall goal of addressing membrane heterogeneities, we performed z-scan FCS (zFCS) of the serotonin(1A) receptor. We analyzed the results according to FCS diffusion laws that provide information on the organization of the diffusing species. Analysis of our results shows that the diffusion coefficients of the receptor and a fluorescently labeled phospholipid are similar when probed at length scales approximately 210 nm. We discuss the significance of the spatiotemporal evolution of dynamics of membrane-bound molecules in the overall context of membrane domains and heterogeneity. Importantly, our results show that the serotonin(1A) receptor exhibits confinement in cell membranes, possibly due to interaction with the actin cytoskeleton. Surprisingly, depletion of membrane cholesterol appears to reduce receptor confinement in a manner similar to that observed in the case of cytoskeletal destabilization, implying possible changes in the actin cytoskeleton induced upon cholesterol depletion. These results constitute the first report on G-protein-coupled receptor dynamics utilizing a combination of zFCS and the FCS diffusion laws, and present a convenient approach to explore cell membrane heterogeneity at the submicron level.

Surface-coupled proton exchange of a membrane-bound proton acceptor

Proton-transfer reactions across and at the surface of biological membranes are central for maintaining the transmembrane proton electrochemical gradients involved in cellular energy conversion. In this study, fluorescence correlation spectroscopy was used to measure the local protonation and deprotonation rates of single pH-sensitive fluorophores conjugated to liposome membranes, and the dependence of these rates on lipid composition and ion concentration. Measurements of proton exchange rates over a wide proton concentration range, using two different pH-sensitive fluorophores with different pK(a)s, revealed two distinct proton exchange regimes. At high pH (> 8), proton association increases rapidly with increasing proton concentrations, presumably because the whole membrane acts as a proton-collecting antenna for the fluorophore. In contrast, at low pH (< 7), the increase in the proton association rate is slower and comparable to that of direct protonation of the fluorophore from the bulk solution. In the latter case, the proton exchange rates of the two fluorophores are indistinguishable, indicating that their protonation rates are determined by the local membrane environment. Measurements on membranes of different surface charge and at different ion concentrations made it possible to determine surface potentials, as well as the distance between the surface and the fluorophore. The results from this study define the conditions under which biological membranes can act as proton-collecting antennae and provide fundamental information on the relation between the membrane surface charge density and the local proton exchange kinetics.

New insights into F-pilus structure, dynamics, and function

F-pili are thin, flexible filaments elaborated by F(+) cells of Escherichia coli. They belong to the class of Gram-negative pili that function in horizontal gene transfer. F-pili are initially required to establish contacts between DNA donor and recipient cells. Beyond that, F-pilus function, and that of other conjugative pili, has remained obscure and controversial. The idea that F-pili are dynamic structures was proposed 40 years ago. Initially, F-pili were thought to remain extended until another cell bound to the filament tip, whereupon the filament retracted to bring the contacted cell to the donor cell surface. Thereafter, secure surface-surface contacts would allow efficient DNA transfer. A later variant of this hypothesis was that F-pili are inherently dynamic, elongating and retracting even in the absence of exogenous signals. A very different hypothesis, also proposed first about 40 years ago, was that F-pili are conduits, presumably passive, for the transfer of DNA from donor to recipient. In this hypothesis, DNA transfer is not obligatorily coupled to F-pilus retraction. Here, we review recent data obtained by integrating long-established facts about the biology of F-pili with modern tools of fluorescence and electron microscopy. These data suggest that one function for F-pili is to search a large volume around donor cells in liquid culture for the presence of other cells. However, this may not be the only function. We show that F-pilin is also required at a second, largely undefined step occurring after cells have been brought into direct contact by F-pilus retraction.

Ligands, their receptors and ... plasma membranes

Ligand-receptor interactions are customarily described by equations that apply to solutes. Yet, most receptors are present in cell membranes so that sufficiently lipophilic ligands could reach the receptor by a two-dimensional approach within the membrane. As summarized in this review, this may affect the ligand-receptor interaction in many ways. Biophysicians calculated that, compared to a three-dimensional approach from the liquid phase, such approach could alter the time the ligands need to find a receptor. Biochemists found that ligand incorporation in lipid bilayers modifies their conformation. This, along with the depth at which the ligands reside in the bilayer, will affect the probability of successful receptor interaction. Novel mechanisms were also introduced, including "exosite" binding and ligand translocation between the receptor's alpha-helical transmembrane domains. Pharmacologists focused attention at ligand concentrations in membrane, their adsorption and release rates and the effects thereof on ligand potency and residence time at the receptor.

Molecular mechanisms for the persistent bronchodilatory effect of the beta 2-adrenoceptor agonist salmeterol

BACKGROUND

Beta(2)-adrenoceptor agonists are effective bronchodilators. In vitro studies demonstrated long-lasting airway smooth muscle relaxation by salmeterol after washout, the quick disappearance of this effect in presence of antagonists and its recovery after antagonist removal. Current explanations invoke salmeterol accumulation in the membrane ('diffusion microkinetic' model) or the existence of salmeterol-binding 'exosites'. An alternative model based on 'rebinding' of a dissociated ligand to the receptor molecules also produces an apparent decrease in the ligand's dissociation rate in the absence of competing ligands. PURPOSE AND APPROACH: Computer-assisted simulations were performed to follow the receptor-occupation by a salmeterol-like ligand and a competing ligand as a function of time. The aptness of the models to describe the above in vitro findings was evaluated.

KEY RESULTS

The 'diffusion microkinetic' model is sufficient to explain a long-lasting beta(2)-adrenoceptor stimulation and reassertion as long as the membrane harbors a high concentration of the agonist. At lower concentration, 'rebinding' and, in second place, 'exosite' binding are likely to become operational.

CONCLUSIONS AND IMPLICATIONS

The 'rebinding' and 'exosite' binding mechanisms take place at a sub-cellular/molecular scale. Pending their demonstration by experiments on appropriate, simple models such as intact cells or membranes thereof, these mechanisms remain hypothetical in the case of salmeterol. Airway smooth muscle contraction could also be governed by additional mechanisms that are particular to this macroscopic approach.

Diffusion in a fluid membrane with a flexible cortical cytoskeleton

We calculate the influence of a flexible network of long-chain proteins, which is anchored to a fluid membrane, on protein diffusion in this membrane. This is a model for the cortical cytoskeleton and the lipid bilayer of the red blood cell, which we apply to predict the influence of the cytoskeleton on the diffusion coefficient of a mobile band 3 protein. Using the pressure field that the cytoskeleton exerts on the membrane, from the steric repulsion between the diffusing protein and the cytoskeletal filaments, we define a potential landscape for the diffusion within the bilayer. We study the changes to the diffusion coefficient on removal of one type of anchor proteins, e.g., in several hemolytic anemias, as well as for isotropic and anisotropic stretching of the cytoskeleton. We predict an overall increase of the diffusion for a smaller number of anchor proteins and increased diffusion for anisotropic stretching in the direction of the stretch, because of the decrease in the spatial frequency as well as in the height of the potential barriers.

Signature of low-dimensional diffusion in complex systems

We present a clear signature of the dimensionality of water diffusion in a powder sample of a synthetic hectorite (a model clay), by analyzing the corresponding neutron scattering functions. The data follow the theoretical predictions for a powder-averaged two-dimensional diffusion, with a two-dimensional diffusion coefficient of 0.75 x 10(-9) m2 s(-1). Neutron scattering data of bulk water are used as a reference, representing motion in three dimensions. The approach is based on analyzing the scattered intensity at zero energy transfers, along with the broadening of the scattering functions, collected at a wide range of energy resolutions. The mathematical relationship between these two quantities follows, for a given shape of the resolution function, a universal master curve, independent of the diffusion coefficient, but strongly dependent on the dimensionality of the motion, which can thus be determined with clarity.