Rupture Forces Between Biological Receptor and Ligand

Molecular recognition can be defined as strong and specific interactions between two molecules without covalently binding to each other. It is essential for many biochemical processes and is realized by highly specific binding of ligands to their receptors. The high affinity makes it an excellent tool in various types of experiments, for example, in affinity cytochemistry, affinity chromatography, diagnostics, biosensors, targeted drug delivery, and immunoassys. Although various techniques have been used, the specific binding mechanism is still not well understood.

In this work, we applied the hybrid molecular simulation method to simulate a process pulling a biotin molecule out of the binding pocket of the biotin-avidin complex through a harmonic potential applied to a tip. The CHARMM force filed is used to describe interactions among the biotin-avidin complex. Hybrid molecular simulations are carried out at the same time scale as that of AFM experiments of single molecular recognition. The changes of the interaction network in the binding complex are recorded and characterized during unbinding by monitoring these observables as a function of tip position: the force applied to biotin, formation and rupture of hydrogen bonds, interactions between biotin and individual residues in the binding pocket. The binding force and unbinding pathways are extracted from MD simulations. This study will provide information on detailed conformations that are hardly observed in single molecular AFM experiments and guide one to design ligands for a variety of applications.


MD Simulation Method and Preliminary Results:

The hybrid MD method is schematically shown in Figure 1. In MD simulations, the tip is pulled at the the time scale of micrometer/second, which mimics AFM experiments.

Figure 1. Hybrid MD simulation for biotin-avidin complex


Figure 2. A typical pulling force-distance curve of biotin-avidin complex from a hybrid MD simulation.


Figure 3. Unbinding pathway


Figure 4. Detail configurations of biotin and surrounding polar (left panel) and non-polar (right panel) residues. Biotin molecules are in red and residues are in other colors.