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.energy landscape ͉ protein folding ͉ conformational transition ͉ principle of minimal frustration ͉ protein function T he concept of a funneled energy landscape explains how proteins fold efficiently into a unique native conformation (1-5). A protein can fold by multiple routes in a diffusive process. Within a long evolutionary period, the shape of the energy landscape has been sufficiently smoothened to permit protein function despite environmental changes or mutations. In a funneled landscape, native interactions dominate the folding funnel, making the bias sufficiently large toward the native conformation compared with the roughness that arises from local minima. Going beyond folding, recent work has included multiple folding basins to describe conformational transitions of proteins that regulate molecular processes in biological systems or can explain, for example, the aggregation of prions (6). Approaches include thermodynamic weighting of different potentials (7), coupling of potentials (8), switching of the Hamiltonian (9), and reconstruction of contact maps (10).This article is focused on the development and application of a dual-funneled energy landscape to understand a protein's mutational behavior.The protein under investigation, the Rop-dimer (repressor of primer, Rop § ), regulates ColE1 plasmid replication in Escherichia coli through RNA binding (11)(12)(13)(14). This homodimer shows abnormal mutational behavior, as discussed below. For an interpretation within the framework of a minimally frustrated energy landscape, one must consider the symmetry of the dimer. Each monomer consists of a helix-turn-helix...

Biophysics of protein evolution and evolutionary protein biophysics

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Interdomain communication revealed in the diabetes drug target mitoNEET

“…Structure-based models have proven to be informative in the mechanism of assembly of a number of proteins (17,31,32). For example, we explain the rop dimer switch between syn and anti structures as a dual basin landscape that corresponds to distinct but related structures (33,34). The unusual strand swap in mitoNEET creates a large interface surface between the two protomers.…”

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

“…54,55 Similar schemes for combining more than one structure-based model have been proposed based on quantum mechanical mixing 56,57 or by combining contacts from different models in a pairwise fashion. 58,59 The advantage of the present formulation is that it does not sacrifice the cooperative formation of folded structures, and allows an arbitrary number of different conformations to be included easily. Multi-Gō models of various flavours have been successfully applied to the study of problems such as conformational transitions in adenylate kinase, 56, 60-62 calmodulin 55,58 and glutaminebinding protein, 57 base-flipping in B-DNA, 63 activation of src-kinase, 64 conformational exchange between different protein folds, 59, 65 structural transitions in motor proteins, 66 and protein binding mechanisms.…”