Allostery and hydration dynamics: a molecular dynamics study of dihydrofolate reductase

Allostery is a biological phenomenon which is displayed in many different proteins, and consists in any kind of coupling between the active site of the protein and a distant site. There is no unique way to identify allosteric sites, even with experimental analyses. This work, by means of Molecular Dynamics simulations, will focus on dihydrofolate reductase (DHFR). We attempt to identify a link between two different classes of amino acids. The first are called sectors: they were obtained by evolutionary data and have been shown to have strong superpositions to allosteric sites. The second ones display a coupling to the catalytic activity of the protein, and were obtained in this work by means of molecular dynamics simulations. We show that the couplings in the second class of amino acids are quite small, but we obtain that coupled sites are connected, in a network-like way, to sectors. Moreover, we analysed, by means of simulations, the first hydration shell of DHFR, in order to verify if sectors show peculiar hydration properties. We show that there exists a strong connection between amino acids around which the reorientational times of water are largest, and sectors. If the results can be generalized to other proteins, it would be possible to make predictions of allosteric sites only by analyzing the protein hydration shells by means of simulations.