No abstract

The pyruvate dehydrogenase multienzyme complex from E. coli shows a sigmoidal dependency of the reaction rate on the substrate concentration when product formation is followed in the presence of physiological concentrations of the cofactor thiamin diphosphate. To elucidate the molecular mechanism of this regulation, the influence of the substrate pyruvate on the coenzyme-protein interaction has been investigated using several coenzyme analogues. The observed binding constants of all coenzymatically active analogues are increased in the presence of the substrate pyruvate, whereas those of all coenzymatically inactive analogues are not altered in the presence of pyruvate. This points to an increased binding affinity of a reaction-intermediate-coenzyme complex to the protein. Since cofactor binding and dissociation at physiological concentrations of thiamin diphosphate are slow compared to the catalytic reaction, a slow transition to the active state of the enzyme occurs. After lowering the pyruvate concentration, the opposite effect, a dissociation of the thiamin diphosphate from the enzyme is observed. This slow substrate dependent enhancement of cofactor binding enables efficient regulation of the pyruvate dehydrogenase complex by its substrate pyruvate.

The structures produced by a sharp tip scraping a compliant surface are modeled in the illustrative case of scan patterns formed by a series of parallel lines. This is made possible by a modified version of the Prandtl model for stick-slip friction, with an interaction energy landscape replicating the morphology of the evolving surface. As a result, a ripple motif emerges with a tilt angle increasing linearly with the distance between the scan lines, except for the region close to the left boundary of the scanned area, where the ripples are oriented at 90°. This region can penetrate considerably to the right, forming a complex branched pattern. These predictions are substantiated by atomic force microscopy nanolithography experiments on polystyrene surfaces at room temperature. A simple and robust theoretical protocol for reproducing earlystage wear processes (potentially going beyond single contacts) is thus made available.