Peptide-Plane Dynamics in Protein Loops from Microsecond Molecular Dynamics. II. Insights on Conformational Restructuring.

Article I introduced a motif-level framework for analyzing molecular dynamics (MD) backbone-dihedral trajectories, using structural motifs extending beyond a single residue as fundamental units of description. Here, Article II combines this motif-level representation with conventional backbone-dihedral-angle analysis to investigate conformational restructuring in protein loops. The peptide planes of the loop residues in the Rho GTPase-binding domain of plexin-B1 (RBD) serve as representative structural motifs. The two components of the combined analysis provide complementary information: conventional (Ψ, Φ)-based analysis identifies local conformational changes, whereas motif-level analysis reveals which peptide planes move in concert and how the restructuring is organized. Importantly, this formulation also provides motif-specific structural, thermodynamic, and ordering properties─local orientational potentials, probability distributions, order parameters, and entropy─expressed in the natural orientational coordinates, (θ, φ), of the structural motif under consideration. Such information is inaccessible from conventional (Ψ, Φ)-based analysis alone. Across the examples examined, a common picture emerges: distinct local conformational changes in protein loops can be realized through dynamically correlated motions of peptide planes within the scope of which the conventional and motif-level analyses connect residue-specific structural transitions with their collective structural, energetic, entropic, and ordering organization. This provides a common basis for analyzing several distinct mechanisms of conformational restructuring in the RBD, the RBD dimer, and the RBD-GTPase Rac1 complex (RBD-Rac1). The K50-G51 peptide plane of the RBD undergoes canonical type-II-to-type-I β-turn crankshaft flips, whereas the corresponding transitions in RBD-Rac1 are more intricate and noncanonical. Deviations from canonical helicity and their subsequent relaxation are characterized. In the RBD dimer, the analysis reveals a concerted dynamical process involving multiple peptide planes. A versatile dynamic hinge and through-space dynamical correlations are also identified. Importantly, the entropic contributions to the free energy differences associated with RBD dimerization and RBD-Rac1 binding are assessed.