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Pupil size and decision making, timing evolutionary innovation and understanding ATP allosteric functions: the PLOS Comp Biol September issue

Here’s our pick of the highlights from September’s PLOS Computational Biology.

The precision with which people make decisions can be predicted by measuring pupil size before they are presented with any information about the decision. According to Peter Murphy and colleagues, spontaneous, moment-to-moment fluctuations in pupil size can predict how a selection of participants varied in their successful decision making. A larger pupil size indicated poorer upcoming task performance, due to more variability in the decisions made once the relevant information was presented. The authors also found that certain individuals who had the largest pupils overall also tended to be the least consistent in their decisions.

Our September issue image: Matching drug binding pockets in protein models using sequence order-independent structure alignments. Image Credit: Michal Brylinski.
Our September issue image: Matching drug binding pockets in protein models using sequence order-independent structure alignments. Image Credit: Michal Brylinski.

Evolutionary adaptation can be described as a biased, stochastic walk of a population of sequences in a high dimensional sequence space. The population explores a fitness landscape and the mutation-selection process biases the population towards regions of higher fitness. Krishnendu Chatterjee and colleagues estimate the time scale that is needed for evolutionary innovation, using the length of the genetic sequence that needs to be adapted as their key parameter. The authors show that a variety of evolutionary processes take exponential time in sequence length, and propose a specific process, ‘regeneration processes’, which allows evolution to work on polynomial time scales. In this view, evolution can solve a problem efficiently if it has solved a similar problem already.

Endogenous adenosine-5’-triphosphate (ATP) can be regarded as a substrate and an allosteric modulator in cellular signal transduction. By analysing the properties of allosteric and substrate ATP-binding sites, Shaoyong Lu and colleagues found that the allosteric ATP-binding sites are less conserved than the substrate ATP-binding sites. Allosteric ATP molecules adopt both compact and extended conformations in the allosteric binding sites, while substrate ATP molecules adopt extended conformations in the substrate binding sites. The authors’ results provide an overall understanding of ATP allosteric functions responsible for regulation in biological systems.

 

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