Early unfolding response of a stable protein domain to environmental changes

The X-ray crystal structure of γ-carboxyglutamic acid (Gla) domains is well-established. These domains are stable to long all-atom simulations in explicit solvent. Here we extend a prior simulation on the Gla domain of factor Vila, an essential vitamin K-dependent protein involved in the initiation of blood coagulation, to ∼20 ns in order to establish a reference point. We also subject this domain to a set of rational environmental changes using molecular dynamics techniques that accommodate long-range electrostatics accurately: (a) we move the seven bound calcium ions to > 17.5 Åfrom any Gla residue and then simulate for 25 ns, and (b) in a separate calculation, we change all of the calcium ions to sodium ions and simulate for 20 ns. For both perturbed systems, the N-terminus chelation complex is initially greatly weakened, leading to increased motion of the ω loop (residues 1-11). In technique a, most calcium ions return to the preperturbation coordinating units within the time scale of the simulation. We track and display the sequence of calcium ion rebinding. The response of this complex, nonstandard system to the perturbations as estimated by accurate all-atom dynamics gives new details on the degree of sampling in early refolding events.