Investigating the conformational preferences of transforming growth factor-β isoforms using targeted molecular dynamics simulations

We study the conformational preferences and mechanical properties of two isoforms of the cytokine transforming growth factor-β (-β1 and -β3) with atomistic detail and including the effects of explicit water. Targeted molecular dynamics simulations are used to perturb experimental “closed” conformations of both proteins into an “open” conformation, thus far only observed crystallographically for one of the two isoforms. The artificial restraints imposed by the protocol are later released, allowing the two covalently bound units of each homodimer to relax. Homology models of the two proteins are also constructed using the other as a template; models that are later subjected to the same process of perturbation into the open conformation and relaxation. On release, both simulations of transforming growth factor-β1 show a tendency to snap back toward the closed conformation, while those of transforming growth factor-β3 remain open for the remainder of the simulation, apparently consistent with measurements from a variety of experimental sources. Duplication of the simulations affords confidence that this observation reflects a genuine effect of the sequence, as opposed to an artifact of the conformations selected at the outset. The study provides a previously unseen level of detail, describing the structural and dynamic behavior of these proteins in solution, and brings us a step closer to understanding the complex relationship between sequence, structure, and signaling in this family of cytokines.