Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack

The coiled‐coil stability and rigidity may be of importance for molecular electronics (electronically bistable molecules). The coiled‐coil binding free energy has been calculated using molecular dynamics (MD). The energy has been computed as a difference of the appropriate free energies; derived for the coiled‐coil and isolated α‐helices separately. All MD simulations have been performed using an explicit model of the solvent, whereas the continuum solvent approach has been applied to analyze the MD trajectories. The computed stability of the coiled‐coil is of the order of −87 kcal/mol, i.e., about −1.2 kcal/mol per amino acid residue, and arises mainly from the electrostatic interactions and hydrophobic effect. The entropy term has been roughly estimated to be of the order of −22 kcal/mol. This assures that coiled‐coil polypeptides may be used as a stable molecular scaffolding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 106–110, 2002