Dynamic remodelling of disordered protein aggregates is an alternative pathway to achieve robust self-assembly of nanostructures

Abstract

Clathrin is a naturally evolved protein that robustly assembles and disassembles into nanoscale spherical cages. This ability to reorganize in a highly dynamic fashion makes clathrin an attractive model system to study the kinetic and thermodynamic principles of biomolecular self-assembly. Through a combination of experimental and computational approaches, we demonstrate that competition between weak non-specific and specific reversible interactions can dictate the initial pathway of the assembly process, yet the final assembled structures are not sensitive to this competition. We conclude that the relative strengths of non-specific and specific interactions control clathrin assembly at short time scales resulting in either disordered protein aggregates or regularly structured assemblies. However with sufficient time for remodeling, the final assembled structure is robustly formed due to geometric constraints arising from specific molecular recognition events. These data provide insight into naturally evolved biological assembly processes and guidance for the design of engineered systems to achieve robust assembly.

Control of self-assembly in micro- and nano-scale systems

“…At pH values below the IEP, the protein quickly forms disordered aggregates in solution that subsequently form cage structures over time due to large-scale remodelling of the clathrin aggregates. Cryo transmission electron microscopy images of clathrin assemblies at pH = 6.0 and pH = 5.1 from [56] clearly show these distinct paths (Fig. 7).…”

“…Three main states were observed during clathrin assembly: monomer, assembled cages, and disordered aggregates. Experimental results from [56] indicate that two distinct kinetic routes occur in clathrin self-assembly. At pH values above the isoelectric point (IEP) of clathrin (pH = 5.8), the assembly proceeds monotonically from monomers to cage structures.…”

“…The prevalence of specific interactions that are weak and reversible, on the other hand, allows dynamic reorganization that can enable systems to explore a wider range of geometric configurations thereby increasing the probability that the thermodynamically favored self-assembly structure will eventually form [56]. Moreover, certain particles have shown the ability to combine local specific order-determining interactions with delocalized non-specific interactions (attraction or repulsion) to achieve robust self-assembly.…”

“…Both of these kinetic routes lead to similar final self-assembled states, which suggests that the mechanism of clathrin assembly has evolved to be robust. Brownian dynamics simulations suggest that stronger non-specific interactions in the system, which are likely caused by clathrin becoming increasingly hydrophobic at pH below the IEP, result in aggregation [56]. These results suggest that non-specific interactions, such as hydrophobic condensation due to local pH changes, can be used as additional degrees of freedom for robustly controlling self-assembly in an open-loop setting (without measurements), and that the use of multiple weak specific interactions can allow the system to escape disordered kinetically trapped states while still forming a desired ordered structure.…”

“…Recently, this behavior was studied with the three-legged protein clathrin, which plays an important role in reshaping the cell membrane during endocytosis [56]. Self-assembly of clathrin is stabilized by multiple (specific) weak leg-leg interactions [57].…”