Allosteric Control of Guanylate Kinase Using Molecular Springs

ABSTRACT In protein dynamics, allosteric regulation is a mechanism in which chemical interaction at an allosteric site, which is to say a site other than the catalytically active protein site, affects the conformation and subsequent function of the protein. Allosteric control is a fundamental control mechanism in cells, especially with regards to enzymes. We use mechanical forces applied to allosteric sites on proteins to mimic a conformational change typically attributed to chemical reactions. In this way, we control the function of the protein with mechanical forces instead of chemical forces. We have attached a semi-rigid DNA polymer to a kinase protein that performs a simple catalytic reaction. This DNA, which acts as a molecular spring, is attached on opposite sides of the soft protein and exerts an outward force on the protein that results in an “open ” and functionally incapacitated conformation. This paper investigates how a DNA-binding agent, ethidium bromide, affects the rigidity of our DNA spring. Previous molecular spring experiments with our DNA-protein chimera recorded inhibition of the protein function by single-stranded (ss) DNA interaction with the protein active site. This inhibitory effect lessens our ability to investigate the relationship between mechanical stress and protein function. This paper also inspects the effect that histones have on removing this functional inhibition. Introduction—Since the advent o