Comparative analysis of adaptor-mediated clathrin assembly reveals general principles for adaptor clustering

Pucadyil, Thomas J.; Holkar, Sachin S.

doi:10.1091/mbc.e16-06-0399

Cited by 17 publications

(23 citation statements)

References 46 publications

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“…BAR domains -bending the membrane inward attracts clathrin aggregates -or mutually repulsive cargo molecules -bending the membrane outward repels clathrin aggregates -(data not shown). A similar disposition of coats to curved membranes is observed in experiments [94]. With increasing time, aggregates continue to grow by binding additional APs and triskelia that form additional rings adjacent to previously formed facets.…”

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confidence: 73%

Modeling the self-assembly of clathrin coats

Giani

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This work is part of the research programme 'Self-assembly of protein coats at membranes' (project nr. 711.012.004) which is financed by the Netherlands Organisation for Scientific Research (NWO). The research described in this thesis was performed using the computational resources of the Computational Biophysics (CBP) group within the MESA+ Institute for Nanotechnology of the University of Twente. SummaryThe assembly of clathrin coats in the presence of adaptor proteins was studied through computer simulations using coarse-grained models and through statistical mechanics. Adopting a reductionist approach based on recent experimental results, we aimed at reproducing and studying the minimal conditions that lead to the successful formation of aggregates, and at investigating the molecular properties and mechanisms required by the assembly process both in bulk conditions and at a membranous surface. In order to tackle this challenging task, coarse-grained models were used to describe all the assembly units involved in the simulations presented in this thesis. These models are based on the available structural data and are engineered to capture the key elements and behavior of the modeled proteins.In Chapter ?? we introduce a coarse grained model of adaptor proteins, inspired by and representing the AP2 complex. The latter, the second most abundant component of endocytic coats after clathrin, is known to play a fundamental role in promoting and assisting the creation of coats at the cytosolic surface of the membrane. It is reported to be able to trigger polymerization of clathrin triskelia in physiological conditions of salt and pH, under which purified clathrin triskelia do not spontaneously self-assemble. The interaction between APs and clathrin were modeled throughout this thesis through a click potential, introduced for the first time in this chapter. The characteristics of the AP model, and of this interaction, have been tuned to reproduce the existing experimental assembly data of an AP2 and clathrin mixture. Our computer simulations provide novel insights into the role of AP2 in the self-assembly of clathrin cages and suggest that the mechanical properties of adaptor proteins are of fundamental importance. In the same chapter, we also developed a statistical mechanical theory that describes the equilibrium concentration of clathrin cages as a function of the other assembly variables and parameters, such as the protein concentrations and interaction strengths.This theoretical model has been further developed in Chapter ??, in order to explicitly take into account the effect of the flexibility of the clathrin triskelion, previously neglected. The main aim of the chapter is to investigate the equilibrium properties of clathrin cages resulting from the aggregation process, with emphasis on their size in the absence and in the presence of adaptor proteins. In order to perform this study, the essential features and characteristics of clathrin and AP2s are captured through a small number of effective parameters, an...

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confidence: 73%

Modeling the self-assembly of clathrin coats

Giani

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“…A powerful aspect of NERDSS is the ability to generate microscopic models where output can be directly compared with experiments of multi-component assembly. Recent in vitro experiments have measured the kinetics of clathrin localization to adaptor-protein coated membranes 29 . We initialize the simulations to match the experiment, with adaptor proteins bound to the membrane surface and a relatively dilute (80nM) but large volume of solution clathrin that is in excess of the membrane surface area (Fig 2).…”

Section: Nerdss Quantifies In Vitro Experiments Of Clathrin Assembly mentioning

confidence: 99%

“…Existing simulations of clathrin-cage assembly provide important physical insight into CME, but they use ad hoc energy-based models that require substantial expertise to develop 11,25,26 , or lack spatial resolution 27,28 . Here we implement an extensible multi-component model of clathrin lattice assembly to quantify distinct pathways and dynamics of assembly in solution and on the membrane, and directly reproduce fluorescence experiments 29 . Our simulations also show how potently the membrane can act to regulate assembly simply through reduction of dimensionality (3D to 2D) 18 .…”

Section: Introductionmentioning

confidence: 99%

“…We develop several models of clathrin lattice assembly, highlighting distinct features of the models that can be used to tune the dynamics and stability of the observed structures. We optimize a clathrin model directly against time-dependent in vitro experimental data of clathrin recruitment and assembly on membranes 29 . We further introduce enzymes to the system to control the lipid populations on the membrane and drive disassembly, capturing driven nonequilibrium dynamics.…”

Section: Introductionmentioning

confidence: 99%

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NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

Varga

Loggia

et al. 2019

Preprint

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Currently, a significant barrier to building predictive models of cell-based self-assembly processes is that molecular models cannot capture minutes-long cellular dynamics that couple distinct components with active processes, while reaction-diffusion models lack sufficient detail for capturing assembly structures. Here we introduce the Non-Equilibrium Reaction-Diffusion Selfassembly Simulator (NERDSS), which addresses this gap by integrating a structure-resolved reaction-diffusion algorithm with rule-based model construction. By representing proteins as rigid, multi-site molecules that adopt well-defined orientations upon binding, NERDSS simulates formation of large reversible structures with sites that can be acted on by reaction rules. We show how NERDSS allows for directly comparing and optimizing models of multi-component assembly against time-dependent experimental data. Applying NERDSS to assembly steps in clathrin-mediated endocytosis, we capture how the formation of clathrin caged structures can be driven by modulating the strength of clathrin-clathrin interactions, by adding cooperativity, or by localizing clathrin to the membrane. NERDSS further predicts how clathrin lattice disassembly can be driven by enzymes that irreversibly change lipid populations on the membrane. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the wide usability and 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.

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“…A similar disposition of coats to curved membranes is observed in experiments. 94 With increasing time, aggregates continue to grow by binding additional APs and triskelia that form additional rings adjacent to previously formed facets. Most lattice patches remain fairly circular; elongated structures arise occasionally, but they often cease to grow and have a tendency to break up into smaller fragments that can grow again.…”

Section: B Formation Of Coated Pitsmentioning

confidence: 99%

Early stages of clathrin aggregation at a membrane in coarse-grained simulations

Giani

Otter

Briels

2017

The Journal of Chemical Physics

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The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

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Comparative analysis of adaptor-mediated clathrin assembly reveals general principles for adaptor clustering

Cited by 17 publications

References 46 publications

Modeling the self-assembly of clathrin coats

Modeling the self-assembly of clathrin coats

NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

Early stages of clathrin aggregation at a membrane in coarse-grained simulations

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