The electrostatic probe: a tool for the investigation of the Aß(1-16) peptide deformations using the static modes.

We investigate the conformational changes of the Amyloid ß(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.

Atomic scale determination of enzyme flexibility and active site stability through static modes: case of dihydrofolate reductase.

A Static Mode approach is used to screen the biomechanical properties of DHFR. In this approach, a specific external stimulus may be designed at the atomic scale granularity to arrive at a proper molecular mechanism. In this frame, we address the issues related to the overall molecular flexibility versus loop motions and versus enzymatic activity. We show that backbone motions are particularly important to ensure DHFR domain communication and notably highlight the role of a α-helix in Met20 loop motion. We also investigate the active site flexibility in different bound states. Whereas in the occluded conformation the Met20 loop is highly flexible, in the closed conformation backbone motions are no longer significant, the Met20 loop is rigidified by new intra- and intermolecular weak bonds, which stabilizes the complex and promotes the hydride transfer. Finally, while various simulations, including I14 V and I14A mutations, confirm that Ile14 is a key residue in catalytic activity, we isolate and characterize at the atomic scale how a specific intraresidue chemical group makes it possible to assist ligand positioning, to direct the nicotinamide ring toward the folate ring.