Protein kinase D1 (PKD1) is a Ser/Thr kinase implicated in a wide variety of cellular responses. PKD1 activation is generally attributed to a PKC-dependent pathway that leads to phosphorylation of the activation loop at Ser(744)/Ser(748). This modification increases catalytic activity, including that toward an autophosphorylation site (Ser(916)) in a postsynaptic density-95/disks large/zonula o...

Graph-theoretical methods for describing complex chemical reactions are reviewed and directed bipartite graphs are found to be the most convenient ones. Subgraphs of reaction intermediates are advocated as a tool for identifying and classifying reaction mechanisms. The notion of reaction intermediate is revisited, and the special class of dualistic intermediates is defined. The topological anal...

There are deep underlying similarities between Rosen’s (M,R) systems as a definition of life and the RAF sets (Reflexive Autocatalytic systems generated by a Food source) introduced by Hordijk and Steel as a way of analyzing autocatalytic sets of reactions. Using RAF concepts we have systematically explored the set of possible small idealized metabolic networks, searching for instances of (M,R)...

This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all t...

Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, identify structural network conditions that guarantee the bifurcation behavior, and develop a method to proper parameters. As relevant example, explicitly provide such parameters Michaelis–Menten Hill Examp...

Kinetic modeling using nonlinear differential equations is proposed to analyze the spontaneous generation of enantiomeric excess in the autocatalytic addition of diisopropylzinc to prochiral pyrimidine carbaldehydes (Soai reaction). Our approach reproduces experimentally observed giant chiral amplification from an initial enantiomeric excess of <10(-6)% to >60%, high sensitivity and positive re...

The directed polymerization of actin networks is an essential element of many biological processes, including cell migration. Different theoretical models considering the interplay between the underlying processes of polymerization, capping, and branching have resulted in conflicting predictions. One of the main reasons for this discrepancy is the assumption of a branching reaction that is eith...