title: Mutations as trapdoors to two competing native conformations of the Rop-dimer.
abstract: Conformational transitions play a central role in regulating protein function. Structure-based models with multiple basins have been used to understand the mechanisms governing these transitions. A model able to accommodate multiple folding basins is proposed to explore the mutational effects in the folding of the Rop-dimer (Rop). In experiments, Rop mutants show unusually strong increases in folding rates with marginal effects on stability. We investigate the possibility of two competing conformations representing a parallel (P) and the wild-type antiparallel (AP) arrangement of the monomers as possible native conformations. We observe occupation of both distinct states and characterize the transition pathways. An interesting observation from the simulations is that, for equivalent energetic bias, the transition to the P basin (non-wild-type basin) shows a lower free-energy barrier. Thus, the rapid kinetics observed in experiments appear to be the result of two competing states with different kinetic behavior, triggered upon mutation by the opening of a trapdoor arising from Rop's symmetric structure. The general concept of having competing conformations for the native state goes beyond explaining Rop's mutational behaviors and can be applied to other systems. A switch between competing native structures might be triggered by external factors to allow, for example, allosteric control or signaling.
authors.affiliation: Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schug
authors.forename: Paul C
authors.initials: PC
authors.lastname: Whitford
authors.forename: Yaakov
authors.initials: Y
authors.lastname: Levy
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D019281:Dimerization; D019143:Evolution, Molecular; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D016601:RNA-Binding Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D016601:RNA-Binding Proteins; C054243:Rop protein, ColE1 plasmid