Raúl Méndez

The eIF-2alpha kinases and the control of protein synthesis.

Protein synthesis is regulated in response to environmental stimuli by covalent modification, primarily phosphorylation, of components of the tranelational machinery. Phosphorylation of the α subunit of eIF‐2 is one of the best‐characterized mechanisms for down‐regulating protein synthesis in higher eukaryotes in response to various stress conditions. Three distinct protein kinases regulate protein synthesis in eukaryotic cells by phosphorylating the α subunit of eIF‐2 at serine‐51. There are two mammalian eIF‐2α kinases: the double‐stranded RNA‐dependent kinase (PKR) and heme‐regulated inhibitor kinase (HRI), and the yeast GCN2. The regulatory mechanisms and the molecular sizes of these eIF‐2α kinases are different. The expression of PKR is induced by interferon, and the kinase activity is stimulated by low concentrations of double‐stranded RNA. HRI is activated under heme‐defi‐cient conditions. Yeast GCN2 is activated by amino acid starvation. The phosphorylation of eIF‐2α results in the shutdown of protein synthesis. Nevertheless, the eIF‐2α kinases can regulate both global as well as specific mRNA translation. Inhibition of protein synthesis correlates with eIF‐2α phosphorylation in response to a wide variety of different stimuli, including heat shock, serum deprivation, glucose starvation, amino acid starvation, exposure to heavy metal ions, and viral infection. Finally, recent studies suggest a role for eIF‐2α phosphorylation in the control of cell growth and differentiation.—de Haro, C., Méndez, R., Santoyo, J. The eIF‐2α kinases and the control of protein synthesis. FASEB J. 10, 1378‐1387(1996)

Mutation bias favors protein folding stability in the evolution of small populations.

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction.

Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation

The molecular clock hypothesis, stating that protein sequences diverge in evolution by accumulating amino acid substitutions at an almost constant rate, played a major role in the development of molecular evolution and boosted quantitative theories of evolutionary change. These studies were extended to protein structures by the seminal paper by Chothia and Lesk, which established the approximate proportionality between structure and sequence divergence. Here we analyse how function influences the relationship between sequence and structure divergence, studying four large superfamilies of evolutionarily related proteins: globins, aldolases, P‐loop and NADP‐binding. We introduce the contact divergence, which is more consistent with sequence divergence than previously used structure divergence measures. Our main findings are: (1) Small structure and sequence divergences are proportional, consistent with the molecular clock. Approximate validity of the clock is also supported by the analysis of the clustering coefficient of structure similarity networks. (2) Functional constraints strongly limit the structure divergence of proteins performing the same function and may allow to identify incomplete or wrong functional annotations. (3) The rate of structure versus sequence divergence is larger for proteins performing different functions than for proteins performing the same function. We conjecture that this acceleration is due to positive selection for new functions. Accelerations in structure divergence are also suggested by the analysis of the clustering coefficient. (4) For low sequence identity, structural diversity explodes. We conjecture that this explosion is related to functional diversification. (5) Large indels are almost always associated with function changes. Proteins 2010.