Date of Award
Doctor of Philosophy (PhD)
More than half a century has passed since the first proposal of a mathematical description of actin filament nucleation and elongation. The kinetics of elongation have been described both mathematically and experimentally, but the kinetics of nucleation remain in question. This work demonstrates that actin filament nucleation is not only thermodynamically unfavorable but also kinetically unfavorable. I used powerful computational methods to analyze the mechanism of actin filament nucleation. I aimed to identify the rate constants responsible for the formation of dimers and trimers that best fit experimental measurements of the concentrations of monomers, polymer, and filament ends over time. The analysis showed that the formation of dimers and trimers is unfavorable because the association reactions are orders of magnitude slower than estimated in previous work, rather than because of rapid dissociation of dimers and trimers. The 95% confidence intervals calculated for the four rate constants were all practically identifiable and spanned no more than one order of magnitude. Slow nucleation reactions are consistent with published high-resolution structures of actin filaments and molecular dynamics simulations of filament ends. One explanation for slow dimer formation, which I support with computational analysis, is the presence of an unfavorable equilibrium. This equilibrium provides for a low concentration of a monomer in a high-energy state necessary for nucleation. The low concentration of this necessary monomeric species gives a slow apparent association rate.
Rosenbloom, Aaron Dovid Tzvi, "Mechanism of Actin Filament Nucleation" (2021). Yale Graduate School of Arts and Sciences Dissertations. 109.