Kinetics Inside the Protein: Shape of the Geminate Kinetics in Myoglobin

Abstract

Synchronized kinetics of ligand binding to a buried active site offers a look inside the protein. Photodissociated ligands are initially alongside their original binding site, so the recombination kinetics describes the trajectory for direct (geminate) rebinding or escape from the protein for the subsequent (bimolecular) rebinding phase. In the model case of myoglobin in water, most of the ligands escape; to better observe the geminate phase, high viscosity cosolvents were used: the kinetics were characterized by multiple barriers and a distribution of rates. An alternative method to enhance the fraction of geminate phase is the application of high pressure which closes the ligand migration channel; in this case of low viscosity without cosolvents, the geminate phase is closer to a simple exponential behavior. Samples with glycerol display the extended geminate kinetics, while samples in water under pressure do not.