Assembly of Viruses and the Pseudo Law of Mass Action

Abstract

that Klenow and Klentaq have minimal sensitivity to pH changes, with proton linkages of ~0.06 and ~0.3 respectively in KCl. Furthermore, osmotic stress data in KCl indicates 500~600 waters are released upon binding by both polymerases. Glutamate is the major intracellular anion accumulated in E.coli in the presence of KCl in the external environment. The 'glutamate effect' is primarily characterized by an increase in DNA binding affinity when chloride is replaced by glutamate. Some proteins also exhibit decreased ionic linkage in glutamate. Klenow exhibits both aspects of the 'glutamate effect'. Substituting glutamate for chloride reduces the ionic linkage for Klenow by >50%. The presence of glutamate also increases the proton linkage of Klenow five fold and decreases water release by ~70% to approximately 150 waters. The dramatic decrease in water release highlights the osmotic nature of the glutamate effect. Glutamate and chloride salts behave as ionic inhibitors of DNA binding but glutamate salts also exhibit an osmotic enhancement effect. While Klentaq's DNA binding affinity is also enhanced by glutamate, its ionic and proton linkages are not altered. The osmotic enhancement is present for Klentaq but it is not as significant in the salt concentration range at which nanomolar Klentaq-DNA binding occurs. E.coli DNA-binding proteins might have evolved to bind tightly at higher salt concentration to utilize the glutamate effect while accumulating intracellular glutamate.

Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaque

“…1 directly model the evolution of the distribution c k (t) that arises ultimately from the distribution of times for each HSC to differentiate or for the progenitor cells to replicate or die. Similar equations have been used to model the evolving distribution of virus capsid sizes [34].…”

“…Since the equations for c k (t) describe the evolution of a distribution, they are sometimes described as Master equations for the underlying process [34,35]. Here we note that the solution to Eqs.…”

Stochastic yield catastrophes and robustness in self-assembly

“…The dynamical properties of the evolution of the polymer-size distribution become evident if the set of ODEs (6) is rewritten as a partial differential equation. This approach was previously described in the context of virus capsid assembly [29,45]. For simplicity, we restrict ourselves to the case L nuc = 2 and let ν 1 = µ and ν ≥2 = ν.…”

Stochastic Yield Catastrophes and Robustness in Self-Assembly

“…Furthermore, it has been observed that nucleation phenomena play a critical role for self-assembly processes 9,10,15,22 . So it is in general necessary to take into account a critical nucleation size, which marks the transition between slow particle nucleation and the faster subsequent structure growth 18,25,28,33 . We denote this critical nucleation size by L nuc , which in terms of classical nucleation theory corresponds to the structure size at which the free energy barrier has its maximum.…”

“…The dynamical properties of the evolution of the polymer-size distribution become evident if the set of ODEs (6) is rewritten as a partial differential equation. This approach was previously described in the context of virus capsid assembly 6,33 .…”