Evolution of catalytic proteins

Abstract

It is believed that all present-day organisms descended from a common cellular ancestor. Such a cell must have evolved from more primitive and simpler precursors, but neither their organization nor the route such evolution took are accessible to the molecular techniques available today. We propose a mechanism, based on functional properties of enzymes and the kinetics of growth, which allows us to reconstruct the general course of early enzyme evolution. A precursor cell containing very few multifunctional enzymes with low catalytic activities is shown to lead inevitably to descendants with a large number of differentiated monofunctional enzymes with high turnover numbers. Mutation and natural selection for faster growth are shown to be the only conditions necessary for such a change to have occurred.

Pathway Evolution by Horizontal Transfer and Positive Selection Is Accommodated by Relaxed Negative Selection upon Upstream Pathway Genes in Purple Bacterial Carotenoid Biosynthesis

“…Current perspectives on the evolution of biosynthetic pathways (reviewed in references 9 and 12) suggest that functional evolution is most commonly due to selection acting on promiscuous protein functions (25,26,65). Particularly interesting in this regard is the emerging "avant-garde view" of proteins (59) whereby conformers (i.e., protein-folding variants) have variable structures in equilibria and perform promiscuous reactions.…”

Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves

“…This is a hallmark of many enzymes of secondary metabolism and contributes to the enormous diversity of products observed (e.g., Gang et al 2002). Only a few modeling studies on such enzymes have been presented so far (Kacser and Beeby 1984;Nuño et al 1997;Zevedei-Oancea 2002, 2004). Although we constructed a simplified, ''skeleton'' model, less than half of the necessary parameters were available or could be derived from the literature.…”

Use of Game-Theoretical Methods in Biochemistry and Biophysics

“…This type of modelling is often based on the assumption that biological systems have been optimised during evolution (cf. [1][2][3][4]). This is in line with Darwin's theory of survival of the fittest.…”

“…This is in line with Darwin's theory of survival of the fittest. In biochemistry, for example, optimality criteria such as maximisation of the adenosine triphosphate (ATP) synthesis flux through a metabolic pathway [1,2,5], thermodynamic efficiency [6], biomass production [4], and minimisation of intermediate concentrations [7] have been proposed and analysed.…”