Proteins on the edge : transitions of structure ensembles in protein unfolding and protein-protein binding

Proteins move. Their incessant fluctuations are governed by a complex interplay between thousands of atoms. Experimental structures, providing exact coordinates for every atom, hence only represent the average of a diverse ensemble of interchanging conformations. Molecular motion is often the barely understood link between structure and biological function. The present work examines two different processes that put proteins on the edge of moving from one global state to another. At the moment of transition, perturbation or, indeed, biological action, benign structure fluctuations can, it seems, turn into major forces. Chains of spectrin repeats apparently rely on structure flexibility to achieve a smooth response to external force. Single molecule atomic force microscopy experiments on this domain, in accord with simulations, showed clear traces of structure fluctuation. On the verge of disruption, thermal fluctuations decide how much extension a spectrin repeat tolerates and whether or not unfolding is blocked by intermediate non-native structures. This picture was supported by experiments and simulations on mutated repeats. The elasticity of the membrane skeleton and, for example, red blood cells, may thus to some extent depend on chaotic motions within single protein domains. Structure fluctuations also affect the process of protein-protein interaction, but the interplay of protein flexibility and recognition remains far from understood. I performed and compared molecular dynamics simulations on 17 protein complexes as well as their free components. Free interaction patches turned out more flexible than the remaining protein surface. However, contrary to common sense, binding does not generally restrict protein flexibility and conformational entropy may be lost but also gained in the process. Current models of recognition do not account for overall protein flexibility or make assumptions that are incompatible with kinetic observations. I combined the simulation data with systematic docking calculations and derived a new model for this process. Often, only subsets of the two free structure ensembles were mutually compatible. A conformer selection step may thus impede the rate of recognition. Protein fluctuations seem to be actively involved in the binding reaction and influence or even control the speed of recognition as well as the stability of the complex.