Lateral movements of membrane glycoproteins restricted by dynamic cytoplasmic barriers

In Memoriam: Mike Sheetz

Michael P. Sheetz made immense contributions to our understanding of motor proteins, membrane biology, cytoskeleton and mechanobiology over his ~50-year career. He started his independent career at the University of Connecticut, after which he moved to Washington University in St. Louis and then to Duke University, where he led the Department of Cell Biology for 10 years. He then moved to Columbia University, where he established a research group focused on mechanobiology, and then founded and led the Mechanobiology Institute at the National University of Singapore for 10 years. He ended his career at the University of Texas Health Center in Galveston, TX, USA. He trained a generation of leading interdisciplinary cell and mechanobiologists whose independent contributions continue to enhance his legacy.

Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization

This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.

Heterogeneity of cell membrane structure studied by single molecule tracking

Heterogeneity in cell membrane structure, typified by microdomains with different biophysical and biochemical properties, is thought to impact on a variety of cell functions. Integral membrane proteins act as nanometre-sized probes of the lipid environment and their thermally-driven movements can be used to report local variations in membrane properties. In the current study, we have used total internal reflection fluorescence microscopy (TIRFM) combined with super-resolution tracking of multiple individual molecules, in order to create high-resolution maps of local membrane viscosity. We used a quadrat sampling method and show how statistical tests for membrane heterogeneity can be conducted by analysing the paths of many molecules that pass through the same unit area of membrane. We describe experiments performed on cultured primary cells, stable cell lines and ex vivo tissue slices using a variety of membrane proteins, under different imaging conditions. In some cell types, we find no evidence for heterogeneity in mobility across the plasma membrane, but in others we find statistically significant differences with some regions of membrane showing significantly higher viscosity than others.

We use total internal reflection fluorescence microscopy combined with super-resolution tracking of multiple individual molecules, in order to create high-resolution maps of local membrane viscosity.

Liquid-Liquid Phase Separation at the Plasma Membrane-Cytosol Interface: Common Players in Adhesion, Motility, and Synaptic Function

Networks of scaffold proteins and enzymes assemble at the interface between the cytosol and specific sites of the plasma membrane, where these networks guide distinct cellular functions. Some of these plasma membrane-associated platforms (PMAPs) include shared core components that are able to establish specific protein-protein interactions, to produce distinct supramolecular assemblies regulating dynamic processes as diverse as cell adhesion and motility, or the formation and function of neuronal synapses. How cells organize such dynamic networks is still an open question. In this review we introduce molecular networks assembling at the edge of migrating cells, and at pre- and postsynaptic sites, which share molecular players that can drive the assembly of biomolecular condensates. Very recent experimental evidence has highlighted the emerging role of some of these multidomain/scaffold proteins belonging to the GIT, liprin-α and ELKS/ERC families as drivers of liquid-liquid phase separation (LLPS). The data point to an important role of LLPS: (i) in the formation of PMAPs at the edge of migrating cells, where LLPS appears to be involved in promoting protrusion and the turnover of integrin-mediated adhesions, to allow forward cell translocation; (ii) in the assembly of the presynaptic active zone and of the postsynaptic density deputed to the release and reception of neurotransmitter signals, respectively. The recent results indicate that LLPS at cytosol-membrane interfaces is suitable not only for the regulation of active cellular processes, but also for the continuous spatial rearrangements of the molecular interactions involved in these dynamic processes.

G protein-coupled receptor-G protein interactions: a single-molecule perspective

G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.

Cellular Membranes, a Versatile Adaptive Composite Material

Cellular membranes belong to the most vital yet least understood biomaterials of live matter. For instance, its biomechanical requirements substantially vary across species and subcellular sites, raising the question how membranes manage to adjust to such dramatic changes. Central to its adaptability at the cell surface is the interplay between the plasma membrane and the adjacent cell cortex, forming an adaptive composite material that dynamically adjusts its mechanical properties. Using a hypothetical composite material, we identify core challenges, and discuss how cellular membranes solved these tasks. We further muse how pathological changes in material properties affect membrane mechanics and cell function, before closing with open questions and future challenges arising when studying cellular membranes.

Principles and Applications of Biological Membrane Organization

Many critical biological events, including biochemical signaling, membrane traffic, and cell motility, originate at membrane surfaces. Each such event requires that members of a specific group of proteins and lipids rapidly assemble together at a specific site on the membrane surface. Understanding the biophysical mechanisms that stabilize these assemblies is critical to decoding and controlling cellular functions. In this article, we review progress toward a quantitative biophysical understanding of the mechanisms that drive membrane heterogeneity and organization. We begin from a physical perspective, reviewing the fundamental principles and key experimental evidence behind each proposed mechanism. We then shift to a biological perspective, presenting key examples of the role of heterogeneity in biology and asking which physical mechanisms may be responsible. We close with an applied perspective, noting that membrane heterogeneity provides a novel therapeutic target that is being exploited by a growing number of studies at the interface of biology, physics, and engineering.

The cortical actin network regulates avidity-dependent binding of hyaluronan by the lymphatic vessel endothelial receptor LYVE-1

Lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) mediates the docking and entry of dendritic cells to lymphatic vessels through selective adhesion to its ligand hyaluronan in the leukocyte surface glycocalyx. To bind hyaluronan efficiently, LYVE-1 must undergo surface clustering, a process that is induced efficiently by the large cross-linked assemblages of glycosaminoglycan present within leukocyte pericellular matrices but is induced poorly by the shorter polymer alone. These properties suggested that LYVE-1 may have limited mobility in the endothelial plasma membrane, but no biophysical investigation of these parameters has been carried out to date. Here, using super-resolution fluorescence microscopy and spectroscopy combined with biochemical analyses of the receptor in primary lymphatic endothelial cells, we provide the first evidence that LYVE-1 dynamics are indeed restricted by the submembranous actin network. We show that actin disruption not only increases LYVE-1 lateral diffusion but also enhances hyaluronan-binding activity. However, unlike the related leukocyte HA receptor CD44, which uses ERM and ankyrin motifs within its cytoplasmic tail to bind actin, LYVE-1 displays little if any direct interaction with actin, as determined by co-immunoprecipitation. Instead, as shown by super-resolution stimulated emission depletion microscopy in combination with fluorescence correlation spectroscopy, LYVE-1 diffusion is restricted by transient entrapment within submembranous actin corrals. These results point to an actin-mediated constraint on LYVE-1 clustering in lymphatic endothelium that tunes the receptor for selective engagement with hyaluronan assemblages in the glycocalyx that are large enough to cross-bridge the corral-bound LYVE-1 molecules and thereby facilitate leukocyte adhesion and transmigration.

Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces

T-cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces increase the lifetimes of stimulatory receptor–ligand bonds (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillar tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillar velocity varies in a ligand-dependent manner; that catch bonds generate responses in which some microvilli almost completely stop, while others move with a broad distribution of velocities; and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T-cells.

The subcellular dynamics of GPCR signaling

G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and mediate the effects of a multitude of extracellular cues, such as hormones, neurotransmitters, odorants and light. Because of their involvement in numerous physiological and pathological processes and their accessibility, they are extensively exploited as pharmacological targets. Biochemical and structural biology investigations have clarified the molecular basis of GPCR signaling to a high level of detail. In spite of this, how GPCRs can efficiently and precisely translate extracellular signals into specific and well-orchestrated biological responses in the complexity of a living cell or organism remains insufficiently understood. To explain the high efficiency and specificity observed in GPCR signaling, it has been suggested that GPCR might signal in discrete nanodomains on the plasma membrane or even form stable complexes with G proteins and effectors. However, directly testing these hypotheses has proven a major challenge. Recent studies taking advantage of innovative optical methods such as fluorescence resonance energy transfer (FRET) and single-molecule microscopy have begun to dig into the organization of GPCR signaling in living cells on the spatial (nm) and temporal (ms) scales on which cell signaling events are taking place. The results of these studies are revealing a complex and highly dynamic picture, whereby GPCRs undergo transient interaction with their signaling partners, membrane lipids and the cytoskeleton to form short-lived signaling nanodomains both on the plasma membrane and at intracellular sites. Continuous exchanges among such nanodomains via later diffusion as well as via membrane trafficking might provide a highly sophisticated way of controlling the timing and location of GPCR signaling. Here, we will review the most recent advances in our understanding of the organization of GPCR signaling in living cells, with a particular focus on its dynamics.

Membrane Lipid Nanodomains

Lipid membranes can spontaneously organize their components into domains of different sizes and properties. The organization of membrane lipids into nanodomains might potentially play a role in vital functions of cells and organisms. Model membranes represent attractive systems to study lipid nanodomains, which cannot be directly addressed in living cells with the currently available methods. This review summarizes the knowledge on lipid nanodomains in model membranes and exposes how their specific character contrasts with large-scale phase separation. The overview on lipid nanodomains in membranes composed of diverse lipids (e.g., zwitterionic and anionic glycerophospholipids, ceramides, glycosphingolipids) and cholesterol aims to evidence the impact of chemical, electrostatic, and geometric properties of lipids on nanodomain formation. Furthermore, the effects of curvature, asymmetry, and ions on membrane nanodomains are shown to be highly relevant aspects that may also modulate lipid nanodomains in cellular membranes. Potential mechanisms responsible for the formation and dynamics of nanodomains are discussed with support from available theories and computational studies. A brief description of current fluorescence techniques and analytical tools that enabled progress in lipid nanodomain studies is also included. Further directions are proposed to successfully extend this research to cells.

Numerical Simulation and FRAP Experiments Show That the Plasma Membrane Binding Protein PH-EFA6 Does Not Exhibit Anomalous Subdiffusion in Cells

The fluorescence recovery after photobleaching (FRAP) technique has been used for decades to measure movements of molecules in two-dimension (2D). Data obtained by FRAP experiments in cell plasma membranes are assumed to be described through a means of two parameters, a diffusion coefficient, D (as defined in a pure Brownian model) and a mobile fraction, M. Nevertheless, it has also been shown that recoveries can be nicely fit using anomalous subdiffusion. Fluorescence recovery after photobleaching (FRAP) at variable radii has been developed using the Brownian diffusion model to access geometrical characteristics of the surrounding landscape of the molecule. Here, we performed numerical simulations of continuous time random walk (CTRW) anomalous subdiffusion and interpreted them in the context of variable radii FRAP. These simulations were compared to experimental data obtained at variable radii on living cells using the pleckstrin homology (PH) domain of the membrane binding protein EFA6 (exchange factor for ARF6, a small G protein). This protein domain is an excellent candidate to explore the structure of the interface between cytosol and plasma membrane in cells. By direct comparison of our numerical simulations to the experiments, we show that this protein does not exhibit anomalous diffusion in baby hamster kidney (BHK) cells. The non Brownian PH-EFA6 dynamics observed here are more related to spatial heterogeneities such as cytoskeleton fence effects.

Supported lipid bilayer platforms to probe cell mechanobiology

Mammalian and bacterial cells sense and exert mechanical forces through the process of mechanotransduction, which interconverts biochemical and physical signals. This is especially important in contact-dependent signaling, where ligand-receptor binding occurs at cell-cell or cell-ECM junctions. By virtue of occurring within these specialized junctions, receptors engaged in contact-dependent signaling undergo oligomerization and coupling with the cytoskeleton as part of their signaling mechanisms. While our ability to measure and map biochemical signaling within cell junctions has advanced over the past decades, physical cues remain difficult to map in space and time. Recently, supported lipid bilayer (SLB) technologies have emerged as a flexible platform to mimic and perturb cell-cell and cell-ECM junctions, allowing one to study membrane receptor mechanotransduction. Changing the lipid composition and underlying substrate tunes bilayer fluidity, and lipid and ligand micro- and nano-patterning spatially control positioning and clustering of receptors. Patterning metal gridlines within SLBs confines lipid mobility and introduces mechanical resistance. Here we review fundamental SLB mechanics and how SLBs can be engineered as tunable cell substrates for mechanotransduction studies. Finally, we highlight the impact of this work in understanding the biophysical mechanisms of cell adhesion. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.

Manipulation and Motion of Organelles and Single Molecules in Living Cells

The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function. In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation and dynamics of single molecule and organelles are reviewed.

Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains

Analysis of high-density superresolution imaging of receptors reveals the organization of dendrites at nanoscale resolution. We present here an apparently novel method that uses local statistics extracted from short-range trajectories for the simulations of long-range trajectories in empirical live cell images. Based on these empirical simulations, we compute the residence time of a receptor in dendritic spines that accounts for receptors' local interactions and geometrical membrane organization. We report here that depending on the type of the spine, the residence time varies from 1 to 5 min. Moreover, we show that there exists transient organized structures, previously described as potential wells that can regulate the trafficking of receptors to dendritic spine: the simulation results suggest that receptor trafficking is regulated by transient structures.

Sensing Size through Clustering in Non-Equilibrium Membranes and the Control of Membrane-Bound Enzymatic Reactions

The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. We show, using stochastic simulations and analytic modeling, that the out-of-equilibrium cluster size distribution of membrane components undergoing continuous recycling is strongly influenced by lateral confinement. This result has significant implications for the clustering of plasma membrane proteins whose mobility is hindered by cytoskeletal “corrals” and for protein clustering in cellular organelles of limited size that generically support material fluxes. We show how the confinement size can be sensed through its effect on the size distribution of clusters of membrane heterogeneities and propose that this could be regulated to control the efficiency of membrane-bound reactions. To illustrate this, we study a chain of enzymatic reactions sensitive to membrane protein clustering. The reaction efficiency is found to be a non-monotonic function of the system size, and can be optimal for sizes comparable to those of cellular organelles.

Simulating Membrane Dynamics in Nonhomogeneous Hydrodynamic Environments

Two previously introduced simulation algorithms for the dynamics of elastic membrane sheets embedded in a fluid medium are extended to account for inhomogeneous hydrodynamic environments. We calculate the height autocorrelation function for a lipid bilayer randomly pinned to a flat substrate and the influence of fluid confinement by the spectrin cytoskeleton on short wavelength membrane undulations of the human red blood cell. Altering the hydrodynamic environment of the membrane leads to significant changes in dynamics, and we discuss these effects in the context of recent experiments.

Cortical actin networks induce spatio-temporal confinement of phospholipids in the plasma membrane--a minimally invasive investigation by STED-FCS

Important discoveries in the last decades have changed our view of the plasma membrane organisation. Specifically, the cortical cytoskeleton has emerged as a key modulator of the lateral diffusion of membrane proteins. Cytoskeleton-dependent compartmentalised lipid diffusion has been proposed, but this concept remains controversial because this phenomenon has thus far only been observed with artefact-prone probes in combination with a single technique: single particle tracking. In this paper, we report the first direct observation of compartmentalised phospholipid diffusion in the plasma membrane of living cells using a minimally invasive, fluorescent dye labelled lipid analogue. These observations were made using optical STED nanoscopy in combination with fluorescence correlation spectroscopy (STED-FCS), a technique which allows the study of membrane dynamics on a sub-millisecond time-scale and with a spatial resolution of down to 40 nm. Specifically, we find that compartmentalised phospholipid diffusion depends on the cortical actin cytoskeleton, and that this constrained diffusion is directly dependent on the F-actin branching nucleator Arp2/3. These findings provide solid evidence that the Arp2/3-dependent cortical actin cytoskeleton plays a pivotal role in the dynamic organisation of the plasma membrane, potentially regulating fundamental cellular processes.

Optical manipulation of single molecules in the living cell

Optical tweezers are the only nano-tools capable of manipulating and performing force-measurements on individual molecules and organelles within the living cell without performing destructive penetration through the cell wall and without the need for inserting a non-endogenous probe. Here, we describe how optical tweezers are used to manipulate individual molecules and perform accurate force and distance measurements within the complex cytoplasm of the living cell. Optical tweezers can grab individual molecules or organelles, if their optical contrast to the medium is large enough, as is the case, e.g., for lipid granules or chromosomes. However, often the molecule of interest is specifically attached to a handle manipulated by the optical trap. The most commonly used handles, their insertion into the cytoplasm, and the relevant micro-rheology of the cell are discussed here and we also review recent and exciting results achieved through optical force manipulation of individual molecules in vivo.

Tracking surface glycans on live cancer cells with single-molecule sensitivity

Using a combination of metabolically labeled glycans, a bioorthogonal copper(I)-catalyzed azide-alkyne cycloaddition, and the controlled bleaching of fluorescent probes conjugated to azide- or alkyne-tagged glycans, a sufficiently low spatial density of dye-labeled glycans was achieved, enabling dynamic single-molecule tracking and super-resolution imaging of N-linked sialic acids and O-linked N-acetyl galactosamine (GalNAc) on the membrane of live cells. Analysis of the trajectories of these dye-labeled glycans in mammary cancer cells revealed constrained diffusion of both N- and O-linked glycans, which was interpreted as reflecting the mobility of the glycan rather than to be caused by transient immobilization owing to spatial inhomogeneities on the plasma membrane. Stochastic optical reconstruction microscopy (STORM) imaging revealed the structure of dynamic membrane nanotubes.

Stresses at the cell surface during animal cell morphogenesis

Cell shape is determined by cellular mechanics. Cell deformations in animal cells, such as those required for cell migration, division or epithelial morphogenesis, are largely controlled by changes in mechanical stress and tension at the cell surface. The plasma membrane and the actomyosin cortex control surface mechanics and determine cell surface tension. Tension in the actomyosin cortex primarily arises from myosin-generated stresses and depends strongly on the ultrastructural architecture of the network. Plasma membrane tension is controlled mainly by the surface area of the membrane relative to cell volume and can be modulated by changing membrane composition, shape and the organization of membrane-associated proteins. We review here our current understanding of the control of cortex and membrane tension by molecular processes. We particularly highlight the need for studies that bridge the scales between microscopic events and emergent properties at the cellular level. Finally, we discuss how the mechanical interplay between membrane dynamics and cortex contractility is key to understanding the biomechanical control of cell morphogenesis.

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.

Single-molecule localization and tracking technique is widely used to visualize molecular dynamics in life science, yet it fails to detect molecular conformation. Serag et al. address this limitation via spatial quantization of temporal fluctuations in the cumulative area occupied by molecules.

Receptor displacement in the cell membrane by hydrodynamic force amplification through nanoparticles

We introduce an intrinsically multiplexed and easy to implement method to apply an external force to a biomolecule and thus probe its interaction with a second biomolecule or, more generally, its environment (for example, the cell membrane). We take advantage of the hydrodynamic interaction with a controlled fluid flow within a microfluidic channel to apply a force. By labeling the biomolecule with a nanoparticle that acts as a kite and increases the hydrodynamic interaction with the fluid, the drag induced by convection becomes important. We use this approach to track the motion of single membrane receptors, the Clostridium perfringens ε-toxin (CPεT) receptors that are confined in lipid raft platforms, and probe their interaction with the environment. Under external force, we observe displacements over distances up to 10 times the confining domain diameter due to elastic deformation of a barrier and return to the initial position after the flow is stopped. Receptors can also jump over such barriers. Analysis of the receptor motion characteristics before, during, and after a force is applied via the flow indicates that the receptors are displaced together with their confining raft platform. Experiments before and after incubation with latrunculin B reveal that the barriers are part of the actin cytoskeleton and have an average spring constant of 2.5 ± 0.6 pN/μm before vs. 0.6 ± 0.2 pN/μm after partial actin depolymerization. Our data, in combination with our previous work demonstrating that the ε-toxin receptor confinement is not influenced by the cytoskeleton, imply that it is the raft platform and its constituents rather than the receptor itself that encounters and deforms the barriers formed by the actin cytoskeleton.

Update of the 1972 Singer-Nicolson Fluid-Mosaic Model of Membrane Structure

The Fluid-Mosaic Membrane Model of cell membrane structure was based on thermodynamic principals and the available data on component lateral mobility within the membrane plane [Singer SJ, Nicolson GL. The Fluid Mosaic Model of the structure of cell membranes. Science 1972; 175: 720-731]. After more than forty years the model remains relevant for describing the basic nano-scale structures of a variety of biological membranes. More recent information, however, has shown the importance of specialized membrane domains, such as lipid rafts and protein complexes, in describing the macrostructure and dynamics of biological membranes. In addition, membrane-associated cytoskeletal structures and extracellular matrix also play roles in limiting the mobility and range of motion of membrane components and add new layers of complexity and hierarchy to the original model. An updated Fluid-Mosaic Membrane Model is described, where more emphasis has been placed on the mosaic nature of cellular membranes where protein and lipid components are more crowded and limited in their movements in the membrane plane by lipid-lipid, protein-protein and lipid-protein interactions as well as cell-matrix, cell-cell and cytoskeletal interactions. These interactions are important in restraining membrane components and maintaining the unique mosaic organization of cell membranes into functional, dynamic domains.

Experimental approaches for addressing fundamental biological questions in living, functioning cells with single molecule precision

In recent years, single molecule experimentation has allowed researchers to observe biological processes at the sensitivity level of single molecules in actual functioning, living cells, thereby allowing us to observe the molecular basis of the key mechanistic processes in question in a very direct way, rather than inferring these from ensemble average data gained from traditional molecular and biochemical techniques. In this short review, we demonstrate the impact that the application of single molecule bioscience experimentation has had on our understanding of various cellular systems and processes, and the potential that this approach has for the future to really address very challenging and fundamental questions in the life sciences.

Control of flux by narrow passages and hidden targets in cellular biology

Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small spatial scales. These may be small binding sites inside or on the surface of the cell, or narrow passages between subcellular compartments. The great disparity in spatial scales is the key to controlling cell function by structure. We report here recent progress on resolving analytical and numerical difficulties in extracting properties from experimental data, from biophysical models, and from Brownian dynamics simulations of diffusion in multi-scale structures. This progress is achieved by developing an analytical approximation methodology for solving the model equations. The reported results are applied to analysis and simulations of subcellular processes and to the quantification of their biological functions.

Lipid bilayer-integrated optoelectronic tweezers for nanoparticle manipulations

Remotely manipulating a large number of microscopic objects is important to soft-condensed matter physics, biophysics, and nanotechnology. Optical tweezers and optoelectronic tweezers have been widely used for this purpose but face critical challenges when applied to nanoscale objects, including severe photoinduced damages, undesired ionic convections, or irreversible particle immobilization on surfaces. We report here the first demonstration of a lipid bilayer-integrated optoelectronic tweezers system for simultaneous manipulation of hundreds of 60 nm gold nanoparticles in an arbitrary pattern. We use a fluid lipid bilayer membrane with a ~5 nm thickness supported by a photoconductive electrode to confine the diffusion of chemically tethered nanoparticles in a two-dimensional space. Application of an external a.c. voltage together with patterned light selectively activates the photoconducting electrode that creates strong electric field localized near the surface. The field strength changes most significantly at the activated electrode surface where the particles tethered to the membrane thus experience the strongest dielectrophoretic forces. This design allows us to efficiently achieve dynamic, reversible, and parallel manipulation of many nanoparticles. Our approach to integrate biomolecular structures with optoelectronic devices offers a new platform enabling the study of thermodynamics in many particle systems and the selective transport of nanoscale objects for broad applications in biosensing and cellular mechanotransductions.

Unraveling novel features hidden in superresolution microscopy data

Stochastic analysis of superresolution microscopy data obtained from receptor trafficking on neurons reveals novel organized molecular assembly generating long range forces. Would that have been possible with single particle tracking? How have we characterized these molecular assemblies?

Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging

Simultaneous tracking of many thousands of individual particles in live cells is possible now with the advent of high-density superresolution imaging methods. We present an approach to extract local biophysical properties of cell-particle interaction from such newly acquired large collection of data. Because classical methods do not keep the spatial localization of individual trajectories, it is not possible to access localized biophysical parameters. In contrast, by combining the high-density superresolution imaging data with the present analysis, we determine the local properties of protein dynamics. We specifically focus on AMPA receptor (AMPAR) trafficking and estimate the strength of their molecular interaction at the subdiffraction level in hippocampal dendrites. These interactions correspond to attracting potential wells of large size, showing that the high density of AMPARs is generated by physical interactions with an ensemble of cooperative membrane surface binding sites, rather than molecular crowding or aggregation, which is the case for the membrane viral glycoprotein VSVG. We further show that AMPARs can either be pushed in or out of dendritic spines. Finally, we characterize the recurrent step of influenza trajectories. To conclude, the present analysis allows the identification of the molecular organization responsible for the heterogeneities of random trajectories in cells.

Antipersistent random walk in a two state flashing magnetic potential

We reveal the subdiffusive dynamics of paramagnetic colloids subjected to a two state flashing potential generated by periodic modulation of a magnetic bubble lattice. The particles perform a random walklike motion with antipersistent nature, showing for certain field parameters a crossover from subdiffusive to an enhanced diffusive behavior. We elucidate the stationary nature (no aging) of the subdiffusive process and stress its similarity with the random walk on a random walk model.

Obstructed diffusion propagator analysis for single-particle tracking

We describe a method for the analysis of the distribution of displacements, i.e., the propagators, of single-particle tracking measurements for the case of obstructed subdiffusion in two-dimensional membranes. The propagator for the percolation cluster is compared with a two-component mobility model against Monte Carlo simulations. To account for diffusion in the presence of obstacle concentrations below the percolation threshold, a propagator that includes the transient motion in finite percolation clusters and hopping between obstacle-induced compartments is derived. Finally, these models are shown to be effective in the analysis of Kv2.1 channel diffusive measurements in the membrane of living mammalian cells.

Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression

Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.

Plasmonic nanoparticle chain in a light field: a resonant optical sail

Optical trapping and driving of small objects has become a topic of increasing interest in multidisciplinary sciences. We propose to use a chain made of metallic nanoparticles as a resonant light sail, attached by one end point to a transparent object and propelling it by the use of electromagnetic radiation. Driving forces exerted on the chain are theoretically studied as a function of radiation's wavelength and chain's alignments with respect to the direction of radiation. Interestingly, there is a window in the frequency spectrum in which null-torque equilibrium configuration, with minimum geometric cross section, corresponds to a maximum in the driving force.

Probing orientational behavior of MHC class I protein and lipid probes in cell membranes by fluorescence polarization-resolved imaging

Steady-state polarization-resolved fluorescence imaging is used to analyze the molecular orientational order behavior of rigidly labeled major histocompatibility complex class I (MHC I) proteins and lipid probes in cell membranes of living cells. These fluorescent probes report the orientational properties of proteins and their surrounding lipid environment. We present a statistical study of the molecular orientational order, modeled as the width of the angular distribution of the molecules, for the proteins in the cell endomembrane and plasma membrane, as well as for the lipid probes in the plasma membrane. We apply this methodology on cells after treatments affecting the actin and microtubule networks. We find in particular opposite orientational order changes of proteins and lipid probes in the plasma membrane as a response to the cytoskeleton disruption. This suggests that MHC I orientational order is governed by its interaction with the cytoskeleton, whereas the plasma membrane lipid order is governed by the local cell membrane morphology.

Narrow escape through a funnel and effective diffusion on a crowded membrane

Particles diffusing on a membrane crowded with obstacles have to squeeze between them through funnel-shaped narrow straits. The computation of the mean passage time through the straits is a new narrow escape problem that gives rise to new, hitherto unknown, behavior that we communicate here. The motion through the straits on the coarse scale of the narrow escape time is an effective diffusion with coefficient that varies nonlinearly with the density of obstacles. We calculate the coarse-grained diffusion coefficient on a planar lattice of circular obstacles and use it to estimate the density of obstacles on a neuronal membrane and in a model of a cytoplasm crowded by identical parallel circular rods.

Detecting nanodomains in living cell membrane by fluorescence correlation spectroscopy

Cell membranes actively participate in numerous cellular functions. Inasmuch as bioactivities of cell membranes are known to depend crucially on their lateral organization, much effort has been focused on deciphering this organization on different length scales. Within this context, the concept of lipid rafts has been intensively discussed over recent years. In line with its ability to measure diffusion parameters with great precision, fluorescence correlation spectroscopy (FCS) measurements have been made in association with innovative experimental strategies to monitor modes of molecular lateral diffusion within the plasma membrane of living cells. These investigations have allowed significant progress in the characterization of the cell membrane lateral organization at the suboptical level and have provided compelling evidence for the in vivo existence of raft nanodomains. We review these FCS-based studies and the characteristic structural features of raft nanodomains. We also discuss the findings in regards to the current view of lipid rafts as a general membrane-organizing principle.

Actin reorganization contributes to loss of cell adhesion in pemphigus vulgaris

In the human autoimmune blistering skin disease pemphigus vulgaris autoantibodies (PV-IgG), which are mainly directed against keratinocyte cell adhesion molecules desmoglein (Dsg) 3 and Dsg1, cause keratinocyte cell dissociation (acantholysis). Recent studies reported that loss of keratinocyte cell adhesion was accompanied by profound alterations of the actin cytoskeleton. Nevertheless, the relevance of actin reorganization in this process is unclear at present. In this study, we provide evidence for an important role of actin reorganization in pemphigus pathogenesis. In parallel to loss of cell adhesion and fragmentation of Dsg3 staining along cell borders, PV-IgG treatment resulted in striking changes in actin cytoskeleton organization. Moreover, in experiments using fluorescence recovery after photobleaching (FRAP), PV-IgG were detected to interfere with actin dynamics. Therefore, we investigated whether pharmacological manipulation of actin polymerization modulates pathogenic effects of PV-IgG. Pharmacological stabilization of actin filaments via jasplakinolide significantly blocked cell dissociation and Dsg3 fragmentation, whereas cytochalasin D-induced actin depolymerization strongly enhanced pathogenic effects of PV-IgG. To substantiate these findings, we studied whether the protective effects of Rho GTPases, which are potent regulators of the actin cytoskeleton and were shown to be involved in pemphigus pathogenesis, were dependent on modulation of actin dynamics. Cytotoxic necrotizing factor-1 (CNF-1)-mediated activation of Rho-GTPases enhanced the cortical junction-associated actin belt and blunted PV-IgG-induced cell dissociation. However, when actin polymerization was blocked under these conditions via addition of latrunculin B, the protective effects of CNF-1 were abrogated. Taken together, these experiments indicate that reorganization of cortical actin filaments is a critical step in PV-IgG-induced keratinocyte dissociation.

Overview of laser microbeam applications as related to antibody targeting

This chapter reviews several techniques which combine the use of laser microbeams with antibodies to study molecular and cellular biology. An overview of the basic properties of lasers and their integration with microscopes and computers is provided. Biophysical applications, such as fluorescence recovery after photobleaching to measure molecular mobility and fluorescence resonance energy transfer to measure molecular distances, as well as ablative applications for the selective inactivation of proteins or the selective killing of cells are described. Other techniques, such as optical trapping, that do not rely on the interaction of the laser with the targeting antibody, are also discussed.

Single mRNA tracking in live cells

Asymmetric distribution of mRNA is a prevalent phenomenon observed in diverse cell types. The posttranscriptional movement and localization of mRNA provides an important mechanism to target certain proteins to specific cytoplasmic regions of their function. Recent technical advances have enabled real-time visualization of single mRNA molecules in living cells. Studies analyzing the motion of individual mRNAs have shed light on the complex RNA transport system. This chapter presents an overview of general approaches for single particle tracking and some methodologies that are used for single mRNA detection.

Insights from a nanoparticle minuet: two-dimensional membrane profiling through silver plasmon ruler tracking

Individual pairs of polymer-tethered silver nanoparticles, so-called silver plasmon rulers, enable distance and orientation measurements on the nanoscale. The reduced linear dichroism and the spectrum of the light scattered from individual plasmon rulers encode information about their orientation and average interparticle separation, respectively. We took advantage of the gain in information silver plasmon rulers offer as probes in optical tracking and analyzed the translational and rotational motions as well as the extension of individual silver plasmon rulers diffusing on the plasma membrane of lysed HeLa cells. Consistent with a compartmentalization of the cell surface on the length scales of the plasmon rulers, most rulers were either immobilized or performed a confined lateral diffusion. Structural details of a plasmon ruler's confinement region became accessible utilizing the orientation and interparticle separation dependent optical response of the plasmon rulers. This approach, which we refer to as polarization-resolved plasmon coupling microscopy, enabled a detailed structural characterization of individual membrane compartments and provided a quantitative metrics to characterize the structural lateral heterogeneity of cell membranes on submicrometer length scales. In combination with adequate tracking methods, the "dance" performed by membrane confined dimers of flexibly linked noble metal nanoparticles revealed deep insight into the underlying membrane morphology.

Microengineered platforms for cell mechanobiology

Mechanical forces play important roles in the regulation of various biological processes at the molecular and cellular level, such as gene expression, adhesion, migration, and cell fate, which are essential to the maintenance of tissue homeostasis. In this review, we discuss emerging bioengineered tools enabled by microscale technologies for studying the roles of mechanical forces in cell biology. In addition to traditional mechanobiology experimental techniques, we review recent advances of microelectromechanical systems (MEMS)-based approaches for cell mechanobiology and discuss how microengineered platforms can be used to generate in vivo-like micromechanical environment in in vitro settings for investigating cellular processes in normal and pathophysiological contexts. These capabilities also have significant implications for mechanical control of cell and tissue development and cell-based regenerative therapies.