MOLECULAR-DYNAMICS STUDY OF UNBINDING OF THE AVIDIN-BIOTIN COMPLEX

We report molecular dynamics simulations that induce, over periods of 40-500 ps, the unbinding of biotin from avidin by means of external ha rmonic forces with force constants close to those of AFM cantilevers. The applied forces are sufficiently large to reduce the overall bindin g energy enough to yield unbinding within the measurement time. Our st udy complements earlier work on biotin-streptavidin that employed a mu ch larger harmonic force constant, The simulations reveal a variety of unbinding pathways, the role of key residues contributing to adhesion as well as the spatial range over which avidin binds biotin. In contr ast to the previous studies, the calculated rupture forces exceed by f ar those observed. We demonstrate, in the framework of models expresse d in terms of one-dimensional Langevin equations with a schematic bind ing potential, the associated Smoluchowski equations, and the theory o f first passage times, that picosecond to nanosecond simulation of lig and unbinding requires such strong forces that the resulting protein-l igand motion proceeds far from the thermally activated regime of milli second AFM experiments, and that simulated unbinding cannot be readily extrapolated to the experimentally observed rupture.