Local Ordering at the N–H Sites of the Rho GTPase Binding Domain of Plexin-B1: Impact of Dimerization

We have developed a new molecular dynamics (MD) based method for describing analytically local potentials at mobile N–H sites in proteins. Here we apply it to the monomer and dimer of the Rho GTPase binding domain (RBD) of the transmembrane receptor plexin-B1 to gain insight into dimerization, which can compete with Rho GTPase binding. In our method, the local potential is given by linear combinations, u(DL,K), of the real combinations of the Wigner rotation matrix elements, DL,K, with L = 1–4 and appropriate symmetry. The combination that “fits best” the corresponding MD potential of mean force, u(MD), is the potential we are seeking, u(DL,K – BEST). For practical reasons the fitting process involves probability distributions, Peq ∝ exp(−u), instead of potentials, u. The symmetry of the potential, u(DL,K), may be related to the irreducible representations of the D2h point group. The monomer (dimer) potentials have mostly Ag and B2u (B1u and B2u) symmetry. For the monomer, the associated probability distr...