Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

Abstract

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.

Physics of viral dynamics

“…With further refinement of the existing techniques, as well as the development of new techniques, in the coming years we expect large steps in terms of understanding the dynamical properties of viruses. Examples of potential new physical virology approaches in the experimental fields include developments in optical microscopy that allow for nanometre resolution imaging 158 , or in AFM, allowing the acquisition of millisecond to microsecond height spectroscopy data 159 for real-time assembly studies 43 , 160 . Beyond using such techniques for an improved understanding of assembly and steady-state dynamics, it also would be interesting to perform assembly kinetics experiments in crowded environments, to mimic the actual situation in cells and to reveal whether depletion attraction and other crowding effects alter the results.…”

Control of septum thickness by the curvature of SepF polymers

“…After 30-min incubation at room temperature, an excess of buffer BF was added, and imaging started. Images were taken with a high-speed atomic force microscope (HS-AFM) from RIBM (Japan) operated in amplitude modulation tapping mode in liquid (38,39). Short cantilevers (USC-F1.2-k0.15, Nano-World) with spring constant of 0.15 N/m were used.…”

High-Speed Nanomechanical Mapping of the Early Stages of Collagen Growth by Bimodal Force Microscopy

“…Until the development of high-speed AFM (HS-AFM) it was not possible to follow in real-time and with high-spatial resolution the evolution of those processes. [4][5][6][7][8][9][10][11][12][13][14][15][16] HS-AFM images have a key limitation, the data do not provide information about the mechanical properties of proteins such as the elastic modulus or the loss tangent. High-resolution maps of mechanical properties are obtained by using AFM methods that operate at imaging rates about 100 times slower.…”