Protein folding in high-dimensional spaces:hypergutters and the role of non-native interactions

الأصل · EN

We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy hypersurface that is characterised by the structure of diffusive "hypergutters" as well as the familiar "funnels". Several general predictions result: (1) intermediate subspaces of configurations will always be visited; (2) specific but non-native interactions are important in stabilising these low-dimensional diffusive searches on the folding pathway; (3) sequential barriers will commonly be found, even in "two-state"proteins; (4) very early times will show charactreristic departures from single-exponential kinetics; (5) contributions of non-native interactions to phi-values are calculable, and may be significant. The example of a three-helix bundle is treated in more detail as an illustration. The model also shows that high-dimensional structures provide conceptual relations between the "folding funnel", "diffusion-collision", "nucleation-condensation" and "topomer search" models of protein folding. It suggests that kinetic strategies for fast folding may be encoded rather generally in non-native, rather than native interactions. The predictions are related to very recent findings in experiment and simulation.