A two-step biopolymer nucleation model shows a nonequilibrium critical point

• Published in: The Journal of chemical physics Vol. 153; no. 2; pp. 025102 - 25122
• Main Authors: Taylor, Alexander I. P., Gahan, Lianne D., Chakrabarti, Buddhapriya, Staniforth, Rosemary A.
• Format: Journal Article
• Language: English
• Published: United States 14.07.2020
• Subjects: Biopolymers - chemistry; Kinetics; Models, Chemical; Monte Carlo Method; Polymerization
• ISSN: 0021-9606; 1089-7690
• DOI: 10.1063/5.0009394

Biopolymer self-assembly pathways are complicated by the ability of their monomeric subunits to adopt different conformational states. This means nucleation often involves a two-step mechanism where the monomers first condense to form a metastable intermediate, which then converts to a stable polymer by conformational rearrangement of constituent monomers. Nucleation intermediates play a causative role in amyloid diseases such as Alzheimer’s and Parkinson’s. While existing mathematical models neglect the conversion dynamics, experiments show that conversion events frequently occur on comparable timescales to the condensation of intermediates and growth of mature polymers and thus cannot be ignored. We present a model that explicitly accounts for simultaneous assembly and conversion. To describe conversion, we propose an experimentally motivated initiation-propagation mechanism in which the stable phase arises locally within the intermediate and then spreads by nearest-neighbor interactions, in a manner analogous to one-dimensional Glauber dynamics. Our analysis shows that the competing timescales of assembly and conversion result in a nonequilibrium critical point, separating a regime where intermediates are kinetically unstable from one where conformationally mixed intermediates accumulate. This strongly affects the accumulation rate of the stable biopolymer phase. Our model is uniquely able to explain experimental phenomena such as the formation of mixed intermediates and abrupt changes in the scaling exponent γ, which relates the total monomer concentration to the accumulation rate of the stable phase. This provides a first step toward a general model of two-step biopolymer nucleation, which can quantitatively predict the concentration and composition of biologically crucial intermediates.