Elucidation of the allosteric pathways in proteins is a computational challenge that strongly benefits from combination of atomistic molecular dynamics (MD) simulations and coarse-grained analysis of the complex dynamical network of chemical interactions based on graph theory. Here, we introduce and assess the performances of the dynamical perturbation network analysis of allosteric pathways in a prototypical V-type allosteric enzyme. Dynamical atomic contacts obtained from MD simulations are used to weight the allosteric protein graph, which involves an extended network of contacts perturbed by the effector binding in the allosteric site. The outcome showed good agreement with previously reported theoretical and experimental extended studies and it provided recognition of new potential allosteric spots that can be exploited in future mutagenesis experiments. Overall, the dynamical perturbation network analysis proved to be a powerful computational tool, complementary to other network-based approaches that can assist the full exploitation of allosteric phenomena for advances in protein engineering and rational drug design.

In this work, we designed a simulation protocol to investigate the spectroscopic properties of point defects in sodalite minerals, Na 8 Si 6 Al 6 O 24 Cl 2 , using time-dependent density functional theory. The F-center absorption spectrum and the sulfur impurity's (S 2 − ) fluorescence spectrum were simulated by considering different electrostatic environments around the cluster (embedded cluster model, ECM approach) and by coupling the electronic transition with vibrations obtained at the periodic boundary condition (PBC) level. These results highlight the influence of vibronic coupling in these spectra and of the confinement in the case of S 2 − fluorescence. The performances of 17 density functionals were assessed for the calculation of vertical excitation and emission energies against experimental values; global hybrids and generalized gradient approximation (GGA) gave the best results. The impact of chemical composition on the absorption spectra of the F-center was investigated, allowing the simulation of colors in absorption for 12 materials from the sodalite family.