Clathrin self-assembly involves coordinated weak interactions favorable for cellular regulation

Binding affinities for 2D protein dimerization benefit from enthalpic stabilization

Dimerization underpins all macromolecular assembly processes both on and off the membrane. While the strength of dimerization,K D , is commonly quantified in solution (3D), many proteins like the soluble BAR domain-containing proteins also reversibly dimerize while bound to a membrane surface (2D). The ratio of dissociation constants, h = K D 2 D K D 3 D , defines a lengthscale that is essential for determining whether dimerization is more favorable in solution or on the membrane surface, particularly for these proteins that reversibly transition between 3D and 2D. While purely entropic rigid-body estimates of h apply well to transmembrane adhesion proteins, we show here using Molecular Dynamics simulations that even moderate flexibility in BAR domains dramatically alters the free energy landscape from 3D to 2D, driving enhanced selectivity and stability of the native dimer in 2D. By simulating BAR homodimerization in three distinct environments, 1) solution (3D), 2) bound to a lipid bilayer (2D), and 3) fully solvated but restrained to a pseudo membrane (2D), we show that both 2D environments induce backbone configurations that better match the crystal structure and produce more enthalpically favorable dimer states, violating the rigid-body estimates to drive h ≪ h R I G I D . Remarkably, contact with an explicit lipid bilayer is not necessary to drive these changes, as the solvated pseudo membrane induces this same result. We show this outcome depends on the stability of the protein interaction, as a parameterization that produces exceptionally stable binding in 3D does not induce systematic improvements on the membrane. With h lengthscales calculated here that are well below a physiological volume-to-surface-area lengthscale, assembly will be dramatically enhanced on the membrane, which aligns with BAR domain function as membrane remodelers. Our approach provides simple metrics to move beyond rigid-body estimates of 2D affinities and assess whether conformational flexibility selects for enhanced stability on membranes.

Effective repulsive interaction between Janus polymer-grafted nanoparticles adhering to lipid vesicles

The adhesion of nanoparticles to lipid vesicles causes curvature deformations to the membrane to an extent determined by the competition between the adhesive interaction and the membrane's elasticity. These deformations can extend over length scales larger than the size of a nanoparticle, leading to an effective membrane-curvature-mediated interaction between nanoparticles. Nanoparticles with uniform surfaces tend to aggregate into unidimensionally close-packed clusters at moderate adhesion strengths and endocytose at high adhesion strengths. Here, we show that the suppression of close-packed clustering and endocytosis can be achieved by the surface modification of the nanoparticles into Janus particles where a moiety of their surface is grafted with polymers under a good solvent condition. The osmotic pressure of the polymer brushes prevents membrane wrapping of the nanoparticles' moieties that are grafted with polymers, thus suppressing their endocytosis. Furthermore, a repulsion between polymer brushes belonging to two nearby nanoparticles destabilizes the dimerization of the nanoparticles over a wide range of values of the polymers' molecular weight and grafting density. This surface modification of nanoparticles should allow for reliable, non-close-packed, and tunable self-assemblies of nanoparticles.

Capturing the mechanics of clathrin-mediated endocytosis

Clathrin-mediated endocytosis enables selective uptake of molecules into cells in response to changing cellular needs. It occurs through assembly of coat components around the plasma membrane that determine vesicle contents and facilitate membrane bending to form a clathrin-coated transport vesicle. In this review we discuss recent cryo-electron microscopy structures that have captured a series of events in the life cycle of a clathrin-coated vesicle. Both single particle analysis and tomography approaches have revealed details of the clathrin lattice structure itself, how AP2 may interface with clathrin within a coated vesicle and the importance of PIP2 binding for assembly of the yeast adaptors Sla2 and Ent1 on the membrane. Within cells, cryo-electron tomography of clathrin in flat lattices and high-speed AFM studies provided new insights into how clathrin morphology can adapt during CCV formation. Thus, key mechanical processes driving clathrin-mediated endocytosis have been captured through multiple techniques working in partnership.

Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis

Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at copy numbers within a cell and across cell types varying from hundreds (e.g. auxilin) to millions (e.g. clathrin). These variations contain important information about function, but without integration with the interaction network, they cannot capture how supply and demand for each protein depends on binding to shared and distinct partners. Here we construct the interface-resolved network of 82 proteins involved in CME and establish a metric, a stoichiometric balance ratio (SBR), that quantifies whether each protein in the network has an abundance that is sub- or super-stoichiometric dependent on the global competition for binding. We find that highly abundant proteins (like clathrin) are super-stoichiometric, but that not all super-stoichiometric proteins are highly abundant, across three cell populations (HeLa, fibroblast, and neuronal synaptosomes). Most strikingly, within all cells there is significant competition to bind shared sites on clathrin and the central AP-2 adaptor by other adaptor proteins, resulting in most being in excess supply. Our network and systematic analysis, including response to perturbations of network components, show how competition for shared binding sites results in functionally similar proteins having widely varying stoichiometries, due to variations in both abundance and their unique network of binding partners.

Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Clathrin-coated structures must assemble on cell membranes to internalize receptors, with the clathrin protein only linked to the membrane via adaptor proteins. These structures can grow surprisingly large, containing over 20 clathrin, yet they often fail to form productive vesicles, instead aborting and disassembling. We show that clathrin structures of this size can both form and disassemble spontaneously when adaptor protein availability is low, despite high abundance of clathrin. Here, we combine recent in vitro kinetic measurements with microscopic reaction-diffusion simulations and theory to differentiate mechanisms of stable vs unstable clathrin assembly on membranes. While in vitro conditions drive assembly of robust, stable lattices, we show that concentrations, geometry, and dimensional reduction in physiologic-like conditions do not support nucleation if only the key adaptor AP-2 is included, due to its insufficient abundance. Nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning additional adaptor types are necessary to form lattices successfully and efficiently. We show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of the transient and abortive structures observed in vivo. Lastly, we quantify the cost of bending the membrane under our curved clathrin lattices using a continuum membrane model. We find that the cost of bending the membrane could be largely offset by the energetic benefit of forming curved rather than flat structures, with numbers comparable to experiments. Our model predicts how adaptor density can tune clathrin-coated structures from the transient to the stable, showing that active energy consumption is therefore not required for lattice disassembly or remodeling during growth, which is a critical advance towards predicting productive vesicle formation.

A kinetic view of clathrin assembly and endocytic cargo sorting

Specificity and sensitivity in biochemical reactions can be achieved through regulation of equilibrium binding affinity or through proofreading mechanisms that allow for the dissociation of unwanted intermediates. In this essay, we aim to provide our perspectives on how the concept of kinetic proofreading might apply in the context of cargo sorting in clathrin-mediated endocytosis.

NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale

Currently, a significant barrier to building predictive models of cellular self-assembly processes is that molecular models cannot capture minutes-long dynamics that couple distinct components with active processes, whereas reaction-diffusion models cannot capture structures of molecular assembly. Here, we introduce the nonequilibrium reaction-diffusion self-assembly simulator (NERDSS), which addresses this spatiotemporal resolution gap. NERDSS integrates efficient reaction-diffusion algorithms into generalized software that operates on user-defined molecules through diffusion, binding and orientation, unbinding, chemical transformations, and spatial localization. By connecting the fast processes of binding with the slow timescales of large-scale assembly, NERDSS integrates molecular resolution with reversible formation of ordered, multisubunit complexes. NERDSS encodes models using rule-based formatting languages to facilitate model portability, usability, and reproducibility. Applying NERDSS to steps in clathrin-mediated endocytosis, we design multicomponent systems that can form lattices in solution or on the membrane, and we predict how stochastic but localized dephosphorylation of membrane lipids can drive lattice disassembly. The NERDSS simulations reveal the spatial constraints on lattice growth and the role of membrane localization and cooperativity in nucleating assembly. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.

Dynamic instability of clathrin assembly provides proofreading control for endocytosis

Clathrin-mediated endocytosis depends on the formation of functional clathrin-coated pits that recruit cargos and mediate the uptake of those cargos into the cell. However, it remains unclear whether the cargos in the growing clathrin-coated pits are actively monitored by the coat assembly machinery. Using a cell-free reconstitution system, we report that clathrin coat formation and cargo sorting can be uncoupled, indicating that a checkpoint is required for functional cargo incorporation. We demonstrate that the ATPase Hsc70 and a dynamic exchange of clathrin during assembly are required for this checkpoint. In the absence of Hsc70 function, clathrin assembles into pits but fails to enrich cargo. Using single-molecule imaging, we further show that uncoating takes place throughout the lifetime of the growing clathrin-coated pits. Our results suggest that the dynamic exchange of clathrin, at the cost of the reduced overall assembly rates, primarily serves as a proofreading mechanism for quality control of endocytosis.

Modifying Membrane Morphology and Interactions with DNA Origami Clathrin-Mimic Networks

We describe the triggered assembly of a bioinspired DNA origami meshwork on a lipid membrane. DNA triskelia, three-armed DNA origami nanostructures inspired by the membrane-modifying protein clathrin, are bound to lipid mono- and bilayers using cholesterol anchors. Polymerization of triskelia, triggered by the addition of DNA staples, links triskelion arms to form a mesh. Using transmission electron microscopy, we observe nanoscale local deformation of a lipid monolayer induced by triskelion polymerization that is reminiscent of the formation of clathrin-coated pits. We also show that the polymerization of triskelia bound to lipid bilayers modifies interactions between them, inhibiting the formation of a synapse between giant unilamellar vesicles and a supported lipid bilayer.

Structure and Assembly of Clathrin Cages

The unusual structure of clathrin, combined with its ability to assemble and disassemble rapidly in cells provides a model system for us to learn about the ways in which proteins can contribute mechanically to a functioning cell. In this article, we discuss the structural properties of clathrin cages and the triskelions which assemble to form them. The function of clathrin depends on the structure of these triskelions and the interactions they make both with each other during assembly and with the adaptor protein network that drives coated vesicle formation. The atomic resolution structure of clathrin domains has been revealed by X-ray crystallography while scattering studies have enabled the shape of a triskelion in solution to be deduced. Cryo-electron microscopy maps have shown the secondary structure of entire cages, how individual triskelion legs are arranged to form a cage and enabled some bound adaptor proteins to be located. Cage formation itself is energetically finely balanced and requires specific interactions between triskelion legs to be productive, as biochemical studies and in silico modeling have shown. Theoretical, structural and cell biological investigations over many years have contributed to our knowledge of clathrin structure and assembly. It now remains to determine the precise nature of the interactions which occur between clathrin triskelions, light chain and heavy chain and the adaptor protein network.

Modeling the Self-Assembly of Protein Complexes through a Rigid-Body Rotational Reaction-Diffusion Algorithm

The reaction-diffusion equations provide a powerful framework for modeling nonequilibrium, cell-scale dynamics over the long time scales that are inaccessible by traditional molecular modeling approaches. Single-particle reaction-diffusion offers the highest resolution technique for tracking such dynamics, but it has not been applied to the study of protein self-assembly due to its treatment of reactive species as single-point particles. Here, we develop a relatively simple but accurate approach for building rigid structure and rotation into single-particle reaction-diffusion methods, providing a rate-based method for studying protein self-assembly. Our simplifying assumption is that reactive collisions can be evaluated purely on the basis of the separations between the sites, and not their orientations. The challenge of evaluating reaction probabilities can then be performed using well-known equations based on translational diffusion in both 3D and 2D, by employing an effective diffusion constant we derive here. We show how our approach reproduces both the kinetics of association, which is altered by rotational diffusion, and the equilibrium of reversible association, which is not. Importantly, the macroscopic kinetics of association can be predicted on the basis of the microscopic parameters of our structurally resolved model, allowing for critical comparisons with theory and other rate-based simulations. We demonstrate this method for efficient, rate-based simulations of self-assembly of clathrin trimers, highlighting how formation of regular lattices impacts the kinetics of association.

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

Stoichiometric balance, or dosage balance, implies that proteins that are subunits of obligate complexes (e.g. the ribosome) should have copy numbers expressed to match their stoichiometry in that complex. Establishing balance (or imbalance) is an important tool for inferring subunit function and assembly bottlenecks. We show here that these correlations in protein copy numbers can extend beyond complex subunits to larger protein-protein interactions networks (PPIN) involving a range of reversible binding interactions. We develop a simple method for quantifying balance in any interface-resolved PPINs based on network structure and experimentally observed protein copy numbers. By analyzing such a network for the clathrin-mediated endocytosis (CME) system in yeast, we found that the real protein copy numbers were significantly more balanced in relation to their binding partners compared to randomly sampled sets of yeast copy numbers. The observed balance is not perfect, highlighting both under and overexpressed proteins. We evaluate the potential cost and benefits of imbalance using two criteria. First, a potential cost to imbalance is that ‘leftover’ proteins without remaining functional partners are free to misinteract. We systematically quantify how this misinteraction cost is most dangerous for strong-binding protein interactions and for network topologies observed in biological PPINs. Second, a more direct consequence of imbalance is that the formation of specific functional complexes depends on relative copy numbers. We therefore construct simple kinetic models of two sub-networks in the CME network to assess multi-protein assembly of the ARP2/3 complex and a minimal, nine-protein clathrin-coated vesicle forming module. We find that the observed, imperfectly balanced copy numbers are less effective than balanced copy numbers in producing fast and complete multi-protein assemblies. However, we speculate that strategic imbalance in the vesicle forming module allows cells to tune where endocytosis occurs, providing sensitive control over cargo uptake via clathrin-coated vesicles.

Protein copy numbers are often found to be stoichiometrically balanced for subunits of multi-protein complexes. Imbalance is believed to be deleterious because it lowers complex yield (the dosage balance hypothesis) and increases the risk of misinteractions, but imbalance may also provide unexplored functional benefits. We show here that the benefits of stoichiometric balance can extend to larger networks of interacting proteins. We develop a method to quantify to what degree protein networks are balanced, and apply it to two networks. We find that the clathrin-mediated endocytosis system in yeast is statistically balanced, but not perfectly so, and explore the consequences of imbalance in the form of misinteractions and endocytic function. We also show that biological networks are more robust to misinteractions than random networks when balanced, but are more sensitive to misinteractions under imbalance. This suggests evolutionary pressure for proteins to be balanced and that any conserved imbalance should occur for functional reasons. We explore one such reason in the form of bottlenecking the endocytosis process. Our method can be generalized to other networks and used to identify out-of-balance proteins. Our results provide insight into how network design, expression level regulation, and cell fitness are intertwined.

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.

A cost-benefit analysis of the physical mechanisms of membrane curvature

Many cellular membrane-bound structures exhibit distinct curvature that is driven by the physical properties of their lipid and protein constituents. Here we review how cells manipulate and control this curvature in the context of dynamic events such as vesicle-mediated membrane traffic. Lipids and cargo proteins each contribute energy barriers that must be overcome during vesicle formation. In contrast, protein coats and their associated accessory proteins drive membrane bending using a variety of interdependent physical mechanisms. We survey the energy costs and drivers involved in membrane curvature, and draw a contrast between the stochastic contributions of molecular crowding and the deterministic assembly of protein coats. These basic principles also apply to other cellular examples of membrane bending events, including important disease-related problems such as viral egress.

Micellization model for the polymerization of clathrin baskets

A thermodynamic model is used to investigate the conditions under which clathrin triskelions form polyhedral baskets. The analysis, which is similar to classical methods used to study micelle formation, relates clathrin basket energetics to system parameters linked to triskelial rigidity, the natural curvature of an isolated triskelion, and interactions between triskelial legs in the assembled polyhedra. Mathematical theory predicts that a minimal ("critical") clathrin concentration, C(C), needs to be surpassed in order for basket polymerization to occur, and indicates how C(C), and the amount of polymerized material, depend on the chosen parameters. Analytical expressions are obtained to indicate how changes in the parameters affect the sizes of the polyhedra which arise when the total clathrin concentration exceeds C(C). A continuum analytic approximation then is used to produce numerical results that illustrate the derived dependences.

Clathrin-mediated endocytosis and adaptor proteins

Macromolecules gain access to the cytoplasm of eukaryotic cells using one of several ways of which clathrin-dependent endocytosis is the most researched. Although the mechanism of clathrin-mediated endocytosis is well understood in general, novel adaptor proteins that play various roles in ensuring specific regulation of the mentioned process are being discovered all the time. This review provides a detailed account of the mechanism of clathrin-mediated internalization of activated G protein-coupled receptors, as well as a description of the major proteins involved in this process.

Clathrin-coated vesicles from brain have small payloads: a cryo-electron tomographic study

Clathrin coats, which stabilize membrane curvature during endocytosis and vesicular trafficking, form highly polymorphic fullerene lattices. We used cryo-electron tomography to visualize coated particles in isolates from bovine brain. The particles range from ∼66 to ∼134nm in diameter, and only 20% of them (all ⩾80nm) contain vesicles. The remaining 80% are clathrin "baskets", presumably artifactual assembly products. Polyhedral models were built for 54 distinct coat geometries. In true coated vesicles (CVs), most vesicles are offset to one side, leaving a crescent of interstitial space between the coat and the membrane for adaptor proteins and other components. The latter densities are fewer on the membrane-proximal side, which may represent the last part of the vesicle to bud off. A small number of densities - presumably cargo proteins - are associated with the interior surface of the vesicles. The clathrin coat, adaptor proteins, and vesicle membrane contribute almost all of the mass of a CV, with most cargoes accounting for only a few percent. The assembly of a CV therefore represents a massive biosynthetic effort to internalize a relatively diminutive payload. Such a high investment may be needed to overcome the resistance of membranes to high curvature.

Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy

Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.

Diversity of clathrin function: new tricks for an old protein

Clathrin is considered the prototype vesicle coat protein whose self-assembly mediates sorting of membrane cargo and recruitment of lipid modifiers. Detailed knowledge of clathrin biochemistry, structure, and interacting proteins has accumulated since the first observation, almost 50 years ago, of its role in receptor-mediated endocytosis of yolk protein. This review summarizes that knowledge, and focuses on properties of the clathrin heavy and light chain subunits and interaction of the latter with Hip proteins, to address the diversity of clathrin function beyond conventional receptor-mediated endocytosis. The distinct functions of the two human clathrin isoforms (CHC17 and CHC22) are discussed, highlighting CHC22's specialized involvement in traffic of the GLUT4 glucose transporter and consequent role in human glucose metabolism. Analysis of clathrin light chain function and interaction with the actin-binding Hip proteins during bacterial infection defines a novel actin-organizing function for CHC17 clathrin. By considering these diverse clathrin functions, along with intracellular sorting roles and influences on mitosis, further relevance of clathrin function to human health and disease is established.

Systems biology and physical biology of clathrin-mediated endocytosis

In this review, we describe the application of experimental data and modeling of intracellular endocytic trafficking mechanisms with a focus on the process of clathrin-mediated endocytosis. A detailed parts-list for the protein-protein interactions in clathrin-mediated endocytosis has been available for some time. However, recent experimental, theoretical, and computational tools have proved to be critical in establishing a sequence of events, cooperative dynamics, and energetics of the intracellular process. On the experimental front, total internal reflection fluorescence microscopy, photo-activated localization microscopy, and spinning-disk confocal microscopy have focused on assembly and patterning of endocytic proteins at the membrane, while on the theory front, minimal theoretical models for clathrin nucleation, biophysical models for membrane curvature and bending elasticity, as well as methods from computational structural and systems biology, have proved insightful in describing membrane topologies, curvature mechanisms, and energetics.

Asymmetry as the key to clathrin cage assembly

The self-assembly of clathrin proteins into polyhedral cages is simulated for the first time (to our knowledge) by introducing a coarse-grain triskelion particle modeled after clathrin's characteristic shape. The simulations indicate that neither this shape, nor the antiparallel binding of four legs along the lattice edges, is sufficient to induce cage formation from a random solution. Asymmetric intersegmental interactions, which probably result from a patchy distribution of interactions along the legs' surfaces, prove to be crucial for the efficient self-assembly of cages.

Conformation switching of clathrin light chain regulates clathrin lattice assembly

Clathrin-coated vesicle formation is responsible for membrane traffic to and from the endocytic pathway during receptor-mediated endocytosis and organelle biogenesis, influencing how cells relate to their environment. Generating these vesicles involves self-assembly of clathrin molecules into a latticed coat on membranes that recruits receptors and organizes protein machinery necessary for budding. Here we define a molecular mechanism regulating clathrin lattice formation by obtaining structural information from co-crystals of clathrin subunits. Low resolution X-ray diffraction data (7.9-9.0 A) was analyzed using a combination of molecular replacement with an energy-minimized model and noncrystallographic symmetry averaging. Resulting topological information revealed two conformations of the regulatory clathrin light chain bound to clathrin heavy chain. Based on protein domain positions, mutagenesis, and biochemical assays, we identify an electrostatic interaction between the clathrin subunits that allows the observed conformational variation in clathrin light chains to alter the conformation of the clathrin heavy chain and thereby regulates assembly.

Self-assembly of three-legged patchy particles into polyhedral cages

The self-assembly of rigid three-legged building blocks into polyhedral cages is investigated by patchy particle simulations. A four-site anisotropic interaction potential is introduced to make pairs of overlapping legs bind in an anti-parallel fashion, thereby forming the edges of a polyhedron of pentagons and hexagons. A torsional potential, reflecting an asymmetry or polarity in the legs' binding potential, proves crucial for the successful formation of closed fullerene-like cages. Self-assembly proceeds by a nucleation-and-growth mechanism, with a high success rate of cage closure. The size distribution of the self-assembled buckyballs is largely determined by the pucker angle of the particle. Nature explores a similar building block, the clathrin triskelion, to regulate vesicle formation at the cell membrane during endocytosis.

MHC II and the endocytic pathway: regulation by invariant chain

The major histocompatibility complex (MHC) class I and II molecules perform vital functions in innate and adaptive immune responses towards invading pathogens. MHC class I molecules load peptides in the endoplasmatic reticulum (ER) and display them to the T cell receptors (TcR) on CD8(+) T lymphocytes. MHC class II molecules (MHC II) acquire their peptides in endosomes and present these to the TcR on CD4+ T lymphocytes. They are vital for the generation of humoral immune responses. MHC II assembly in the ER and trafficking to endosomes is guided by a specialized MHC II chaperone termed the invariant chain (Ii). Ii self-associates into a trimer in the ER, this provides a scaffold for the assembly of three MHC II heterodimers and blocks their peptide binding grooves, thereby avoiding premature peptide binding. Ii then transports the nascent MHC II to more or less specialized compartment where they can load peptides derived from internalized pathogens.

Identification of a function-specific mutation of clathrin heavy chain (CHC) required for p53 transactivation

The p53 pathway is activated in response to various cellular stresses to protect cells from malignant transformation. We have previously shown that clathrin heavy chain (CHC), which is a cytosolic protein regulating endocytosis, is present in nuclei and binds to p53 to promote p53-mediated transcription. However, details of the binding interface between p53 and CHC remain unclear. Here, we report on the binding mode between p53 and CHC using mutation analyses and a structural model of the interaction generated by molecular dynamics. Structural modeling analyses predict that an Asn1288 residue in CHC is crucial for binding to p53. In fact, substitution of this Asn to Ala of CHC diminished its ability to interact with p53, leading to reduced activity to transactivate p53. Surprisingly, this mutation had little effect on receptor-mediated endocytosis. Thus, the function-specific mutation of CHC will clarify physiological roles of CHC in the regulation of the p53 pathway.

Architecture of clathrin fullerene cages reflects a geometric constraint--the head-to-tail exclusion rule--and a preference for asymmetry

Fullerene cages have n trivalent vertices, 12 pentagonal faces, and (n-20)/2 hexagonal faces. The smallest cage in which all of the pentagons are surrounded by hexagons and thus isolated from each other has 60 vertices and is shaped like a soccer ball. The protein clathrin self-assembles into fullerene cages of a variety of sizes and shapes, including smaller ones with adjacent pentagons as well as larger ones, but the variety is limited. To explain the range of clathrin architecture and how these fullerene cages self-assemble, we proposed a hypothesis, the "head-to-tail exclusion rule" (the "Rule"). Of the 5769 small clathrin cage isomers with n< or =60 vertices and adjacent pentagons, the Rule permits just 15, three identified in 1976 and 12 others. A "weak version" of the Rule permits another 99. Based on cryo-electron tomography, Cheng et al. reported six raw clathrin fullerene cages. One was among the three identified in 1976. Here, (1) we identify the remaining five. (2) Four are new and are among the 12 others permitted by the Rule. (3) One, also new, is among the 99 weak version cages. (4) Of particular note, none of the remaining 5565 excluded cages has been identified. These findings provide powerful experimental confirmation of the Rule and the principle on which it is based. (5) Surprisingly, the newly identified clathrin cages are among the least symmetric of those permitted. (6) By devising a method for counting assembly paths, (7) we show that asymmetric cages can be assembled by larger numbers of paths, thus providing a kinetic explanation for the prevalence of asymmetric cages. (8) Finally, we show that operation during cage growth of the Rule greatly increases the likelihood of producing a closed fullerene cage, specifically one of those permitted, but efficient assembly still appears to require internal remodeling.

Monomeric but not trimeric clathrin heavy chain regulates p53-mediated transcription

Tumor suppressor p53 protein is the transcription factor responsible for various genes including DNA repair, growth arrest, apoptosis and antiangiogenesis. Recently, we showed that clathrin heavy chain (CHC), which was originally identified as a cytosolic protein regulating endocytosis, is present in nuclei and functions as a coactivator for p53. Here, we determined the detailed p53-binding site of CHC and a CHC deletion mutant containing this region (CHC833-1406) behaved as a monomer in cells. Monomeric CHC833-1406 still had a higher ability to transactivate p53 than wild-type CHC although this CHC mutant no longer had endocytic function. Moreover, similar to wild-type CHC, monomeric CHC enhances p53-mediated transcription through the recruitment of histone acetyltransferase p300. Immunofluorescent microscopic analysis exhibited that CHC833-1406 is predominantly localized in nuclei, suggesting that there may be a certain regulatory domain for nuclear export in the C-terminus of CHC. Thus, the trimerization domain of CHC is not necessary for the transactivation of p53 target genes and these data provide further evidence that nuclear CHC plays a role distinct from clathrin-mediated endocytosis.

A geometric principle may guide self-assembly of fullerene cages from clathrin triskelia and from carbon atoms

Clathrin triskelia and carbon atoms alike self-assemble into a limited selection of fullerene cages (with n three connected vertices, 3n/2 edges, 12 pentagonal faces, and (n-20)/2 hexagonal faces). We show that a geometric constraint-exclusion of head-to-tail dihedral angle discrepancies (DADs)-explains this limited selection as well as successful assembly into such closed cages in the first place. An edge running from a pentagon to a hexagon has a DAD, since the dihedral angles about the edge broaden from its pentagon (tail) end to its hexagon (head) end. Of the 21 configurations of a central face and surrounding faces, six have such DAD vectors arranged head-to-tail. Of the 5770 mathematically possible fullerene cages for n <or= 60, excluding those with any of the six configurations leaves just 15 cages plus buckminsterfullerene (n = 60), among them the known clathrin cages. Of the 216,739 mathematically possible cages for 60 < n <or= 84, just the 50 that obey the isolated-pentagon rule, among them known carbon cages, pass. The absence of likely fullerenes for some n (30,34,46,48,52-58,62-68) explains the abundance of certain cages, including buckminsterfullerene. These principles also suggest a "probable roads" path to self-assembly in place of pentagon-road and fullerene-road hypotheses.

Structural insights into the clathrin coat

Clathrin is a cytoplasmic protein best known for its role in endocytosis and intracellular trafficking. The diverse nature of clathrin has recently become apparent, with strong evidence available suggesting roles in both chromosome segregation and reassembly of the Golgi apparatus during mitosis. Clathrin functions as a heterohexamer, adopting a three-legged triskelion structure of three clathrin light chains and three heavy chains. During endocytosis clathrin forms a supportive network about the invaginating membrane, interacting with itself and numerous adapter proteins. Advances in the field of structural biology have led us to a greater understanding of clathrin in its assembled state, the clathrin lattice. Combining techniques such as X-ray crystallography, NMR, and cryo-electron microscopy has allowed us to piece together the intricate nature of clathrin-coated vesicles and the interactions of clathrin with its many binding partners. In this review I outline the roles of clathrin within the cell and the recent structural advances that have improved our understanding of clathrin-clathrin and clathrin-protein interactions.

Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids

UL25 and UL17 are two essential minor capsid proteins of HSV-1, implicated in DNA packaging and capsid maturation. We used cryo-electron microscopy to examine their binding to capsids, whose architecture observes T = 16 icosahedral geometry. C-capsids (mature DNA-filled capsids) have an elongated two-domain molecule present at a unique, vertex-adjacent site that is not seen at other quasiequivalent sites or on unfilled capsids. Using SDS-PAGE and mass spectrometry to analyze wild-type capsids, UL25 null capsids, and denaturant-extracted capsids, we conclude that (1) the C-capsid-specific component is a heterodimer of UL25 and UL17, and (2) capsids have additional populations of UL25 and UL17 that are invisible in reconstructions because of sparsity and/or disorder. We infer that binding of the ordered population reflects structural changes induced on the outer surface as pressure builds up inside the capsid during DNA packaging. Its binding may signal that the C-capsid is ready to exit the nucleus.

Light chain C-terminal region reinforces the stability of clathrin heavy chain trimers

The self-assembly of clathrin into lattices relies on the ability of heavy chain legs to form a three-legged pinwheel structure. We investigated the role of light chains in clathrin trimerization by challenging recombinant hub (plus and minus light chain) with an anionic detergent. The binding of light chain increases the amount of detergent needed to induce detrimerization, suggesting light chains reinforced hub trimers. We also show that light chain C-terminal residues are important for enhancing the in vitro assembly of hub at low pH. We assessed how much the C-terminus of light chain contributed to the stability of the trimerization domain by adding full-length and truncated light chains to trimer-defective hub mutants, C1573S and C1573A. Adding full-length LCb to C1573S caused some retrimerization, but little activity was restored, suggesting the majority of oligomeric C1573S was nonnative. A larger percentage of monomeric C1573A could be retrimerized into an assembly-competent form by adding intact LCb. We also discovered that C-terminally deleted light chains produced a heterogeneous population of hubs that were smaller than native hubs, but were assembly active. We propose a model showing how light chains reinforce the puckered clathrin triskelion. Finally, the ability of light chains to retrimerize C1573A hub suggests that the structural role of light chain may be conserved in yeast and mammals.

Trimerisation is important for the function of clathrin at the mitotic spindle

Clathrin is a triskelion consisting of three heavy chains each with an associated light chain. During mitosis, clathrin contributes to kinetochore fibre stability. As the N-terminal domain at the foot of each leg can bind to the mitotic spindle, we proposed previously a ;bridge hypothesis' wherein clathrin acts as a brace between two or three microtubules within a kinetochore fibre to increase fibre stability. Here, we have tested this hypothesis by replacing endogenous clathrin heavy chain in human cells with a panel of clathrin constructs. Mutants designed to abolish trimerisation were unable to rescue the mitotic defects caused by depletion of endogenous clathrin. By contrast, stunted triskelia with contracted legs could partially rescue normal mitosis. These results indicate that the key structural features of clathrin that are necessary for its function in mitosis are a trimeric molecule with a spindle interaction domain at each end, supporting the bridge hypothesis for clathrin function in mitosis.

Bending a membrane: how clathrin affects budding

Receptor-mediated endocytosis of ligands, such as transferrin and LDL, is suppressed when clathrin synthesis is blocked by RNA interference in HeLa cells. We have found that domains containing the adapter complex 2 (AP2)-coated vesicle adapter and the endocytic accessory proteins CALM (clathrin assembly lymphoid myeloid leukemia protein), epsin, and eps15/eps15R (EGF receptor pathway substrate 15-related) nevertheless persist at the plasma membrane. They are similar in size and number to those seen in clathrin-expressing cells. Here we characterize these membrane domains by fluorescence and electron microscopy in detail. Fluorescence recovery after photobleaching measurements suggest that the exchange between membrane-bound and free cytosolic AP2 molecules is not significantly influenced by the depletion of clathrin. The AP2 membrane domains are dispersed upon interfering with protein-protein interactions that involve the alpha appendage domain of AP2. Electron microscopy of cellular cortices revealed that the AP2 membrane domains lack any curvature, suggesting that clathrin is essential for driving coated pit invagination. A model for coated vesicle formation, incorporating a mechanism commonly referred to as a "Brownian ratchet," is consistent with our observations.

Measuring the elasticity of clathrin-coated vesicles via atomic force microscopy

Using a new scheme based on atomic force microscopy (AFM), we investigate mechanical properties of clathrin-coated vesicles (CCVs). CCVs are multicomponent protein and lipid complexes of approximately 100 nm diameter that are implicated in many essential cell-trafficking processes. Our AFM imaging resolves clathrin lattice polygons and provides height deformation in quantitative response to AFM-substrate compression force. We model CCVs as multilayered elastic spherical shells and, from AFM measurements, estimate their bending rigidity to be 285 +/- 30 k(B)T, i.e., approximately 20 times that of either the outer clathrin cage or inner vesicle membrane. Further analysis reveals a flexible coupling between the clathrin coat and the membrane, a structural property whose modulation may affect vesicle biogenesis and cellular function.

New Faces of the Familiar Clathrin Lattice

The clathrin triskelion self-assembles into a lattice that coats transport vesicles participating in several key membrane traffic pathways. A new model of a clathrin lattice at approximately 8 angstrom resolution, generated by Fotin et al. (Nature 2004;432:573) confirmed the basic structural features of clathrin that were defined over many years of biochemical and structural analysis. In addition, new structural features of the clathrin trimerization domain were modelled for the first time, and the predictions correlated well with previous biochemical studies. A second model, placing auxilin within the lattice suggested a possible lattice contact targeted during lattice disassembly (Fotin et al. Nature 2004;432:649). This contact predicts interactions of the newly modelled trimerization domain with a newly defined extension of the clathrin triskelion, the ankle domain. These aspects of the new models were emphasized in the published reports describing them and in recent commentary (Brodsky, Nature 2004;432:568). Also emerging from the new models is a better picture of how the clathrin structure is distributed throughout the lattice, allowing the first predictions of interacting molecular interfaces contributing to contacts in the assembled lattice. The focus of this interchange is to emphasize these additional features revealed by the recently published models from Fotin and colleagues.

Highly cooperative control of endocytosis by clathrin

Clathrin assembles into a dynamic two-dimensional lattice on the plasma membrane where it plays a critical role in endocytosis. To probe the regulation of this process, we used siRNA against clathrin, in combination with single cell assays for transferrin uptake as well as total internal reflection microscopy, to examine how endocytic rates and membrane dynamics depend upon cellular clathrin concentration ([Clathrin]). We find that endocytosis is tightly controlled by [Clathrin] over a very narrow dynamic range such that small changes in [Clathrin] can lead to large changes in endocytic rates, indicative of a highly cooperative process (apparent Hill coefficient, n > 6). The number of clathrin assemblies at the cell surface was invariant over a wide range of [Clathrin]; however, both the amount of clathrin in each assembly and the subsequent membrane dynamics were steeply dependent on [Clathrin]. Thus clathrin controls the structural dynamics of membrane internalization via a strongly cooperative process. We used this analysis to show that one important regulator of endocytosis, the actin cytoskeleton, acts noncompetitively as a modulator of clathrin function.

Visualization of the Binding of Hsc70 ATPase to Clathrin Baskets

Clathrin assembly into coated pits and vesicles is promoted by accessory proteins such as auxilin and AP180, and disassembly is effected by the Hsc70 ATPase. These interactions may be mimicked in vitro by the assembly and disassembly of clathrin "baskets." The chimera C58J is a minimal construct capable of supporting both reactions; it consists of the C58 moiety of AP180, which facilitates clathrin assembly, fused with the J domain of auxilin, which recruits Hsc70 to baskets. We studied the process of disassembly by using cryo-electron microscopy to identify the initial binding site of Hsc70 on clathrin-C58J baskets at pH 6, under which conditions disassembly does not proceed further. Hsc70 interactions involve two sites: (i) its major interaction is with the sides of spars of the clathrin lattice, close to the triskelion hubs and (ii) there is another interaction at a site at the N-terminal hooks of the clathrin heavy chains, presumably via the J domain of C58J. We propose that individual triskelions may be extricated from the clathrin lattice by the concerted action of up to six Hsc70 molecules, which intercalate between clathrin leg segments, prying them apart. Three Hsc70s remain bound to the dissociated triskelion, close to its trimerization hub.

Huntingtin Interacting Protein 1 (HIP1) Regulates Clathrin Assembly through Direct Binding to the Regulatory Region of the Clathrin Light Chain

Huntingtin interacting protein 1 (HIP1) is a component of clathrin coats. We previously demonstrated that HIP1 promotes clathrin assembly through its central helical domain, which binds directly to clathrin light chains (CLCs). To better understand the relationship between CLC binding and clathrin assembly we sought to dissect this interaction. Using C-terminal deletion constructs of the HIP1 helical domain, we identified a region between residues 450 and 456 that is required for CLC binding. Within this region, point mutations showed the importance of residues Leu-451, Leu-452, and Arg-453. Mutants that fail to bind CLC are unable to promote clathrin assembly in vitro but still mediate HIP1 homodimerization and heterodimerization with the family member HIP12/HIP1R. Moreover, HIP1 binding to CLC is necessary for HIP1 targeting to clathrin-coated pits and clathrin-coated vesicles. Interestingly, HIP1 binds to a highly conserved region of CLC previously demonstrated to regulate clathrin assembly. These results suggest a role for HIP1/CLC interactions in the regulation of clathrin assembly.

Huntingtin-interacting Protein 1 (Hip1) and Hip1-related Protein (Hip1R) Bind the Conserved Sequence of Clathrin Light Chains and Thereby Influence Clathrin Assembly in Vitro and Actin Distribution in Vivo

Clathrin heavy and light chains form triskelia, which assemble into polyhedral coats of membrane vesicles that mediate transport for endocytosis and organelle biogenesis. Light chain subunits regulate clathrin assembly in vitro by suppressing spontaneous self-assembly of the heavy chains. The residues that play this regulatory role are at the N terminus of a conserved 22-amino acid sequence that is shared by all vertebrate light chains. Here we show that these regulatory residues and others in the conserved sequence mediate light chain interaction with Hip1 and Hip1R. These related proteins were previously found to be enriched in clathrin-coated vesicles and to promote clathrin assembly in vitro. We demonstrate Hip1R binding preference for light chains associated with clathrin heavy chain and show that Hip1R stimulation of clathrin assembly in vitro is blocked by mutations in the conserved sequence of light chains that abolish interaction with Hip1 and Hip1R. In vivo overexpression of a fragment of clathrin light chain comprising the Hip1R-binding region affected cellular actin distribution. Together these results suggest that the roles of Hip1 and Hip1R in affecting clathrin assembly and actin distribution are mediated by their interaction with the conserved sequence of clathrin light chains.

Survey of the year 2003 commercial optical biosensor literature

In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.