Plasticity, evolvability, and modularity in RNA

Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins

Proteins display generic properties that are challenging to explain by direct selection, notably allostery, the capacity to be regulated through long-range effects, and evolvability, the capacity to adapt to new selective pressures. An evolutionary scenario is proposed where proteins acquire these two features indirectly as a by-product of their selection for a more fundamental property, exquisite discrimination, the capacity to bind discriminatively very similar ligands. Achieving this task is shown to typically require proteins to undergo a conformational change. We argue that physical and evolutionary constraints impel this change to be controlled by a group of sites extending from the binding site. Proteins can thus acquire a latent potential for allosteric regulation and evolutionary adaptation because of long-range effects that initially arise as evolutionary spandrels. This scenario accounts for the groups of conserved and coevolving residues observed in multiple sequence alignments. However, we propose that most pairs of coevolving and contacting residues inferred from such alignments have a different origin, related to thermal stability. A physical model is presented that illustrates this evolutionary scenario and its implications. The scenario can be implemented in experiments of protein evolution to directly test its predictions.

Evolution of sparsity and modularity in a model of protein allostery

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary constraints may take is important to interpret the information in protein sequences. To study this problem, we introduce a simple but physical model of protein evolution where selection targets allostery, the functional coupling of distal sites on protein surfaces. This model shows how the geometrical organization of couplings between amino acids within a protein structure can depend crucially on its evolutionary history. In particular, two scenarios are found to generate a spatial concentration of functional constraints: high mutation rates and fluctuating selective pressures. This second scenario offers a plausible explanation for the high tolerance of natural proteins to mutations and for the spatial organization of their least tolerant amino acids, as revealed by sequence analysis and mutagenesis experiments. It also implies a faculty to adapt to new selective pressures that is consistent with observations. The model illustrates how several independent functional modules may emerge within the same protein structure, depending on the nature of past environmental fluctuations. Our model thus relates the evolutionary history of proteins to the geometry of their functional constraints, with implications for decoding and engineering protein sequences.