Simulation of Atomic Force Microscopy Rupture Experiments
The force required to rupture the streptavidin-biotin complex has been studied by computer simulations. The computed forces agree well with those obtained by single molecule atomic force microscope (AFM) experiments. The simulations suggest a multiple pathway rupture mechanism, which depends on the applied loading rate. Binding forces and specificity are attributed to a hydrogen bond network between biotin and streptavidin.
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Multiple simulation studies [Izrailev et al. 1997; Grubmuller et al. 1996; Sieben et al. 2012] aimed at a microscopic interpretation of single molecule AFM experiments, in which unbinding forces between individual protein-ligand complexes have been measured. We asked, what interactions cause the experimentally observed unbinding forces particulary.
The top of Figure 1 sketches a typical AFM rupture experiment: On one side, the molecule of interest is attached to a surface via a linker. On the other side, it is attached to a cantilever by a second linker. When the surface is moved away from the cantilever (indicated by the blue arrow), the cantilever bends and a force can be recorded. At the moment of rupture, the force will abruptly drop down to zero.
For the computer simulations (bottom part of Fig. 1), the complex was fixed on the far end side of the binding site. The cantilever was replaced by a harmonic potential (sketched as a grey spring in the bottom figure) with the same stiffness as the cantilever in the experimental setup. In the latest simulations (Video 4), not only a monomeric streptavidin-biotin complex was simulated but the whole tetramer and the linker between the cantilever and the ligand was modeled by a worm like chain potential with the same characteristics as the PEG linker in the experiments. In contrast to the experimental setup, the center of the harmonic potential was moved away com the complex.
Both the AFM rupture experiments as well as our simulation studies focussed on the streptavidin-biotin complex as a model system for specific ligand binding. Streptavidin is a particularly well-studied protein and binds its ligand biotin with high affinity and specificity.
The computer simulations and AFM experiments were in good agreement and allowed us to describe rupture forces for more than 11 orders of magnitude of loading rates. The combination of the two techniques provided detailed insight into the complex mechanisms of streptavidin-biotin unbinding showing a heterogeneity of unbinding pathways depending on the applied loading rate.
Below, you'll find three movies showing part of a 1 nanosecond molecular dynamics simulation of the rupture process. Three numbers are shown at the bottom of each of the movies, indicating the elapsed time in picoseconds (left side), the distance in angstrom the pulling 'spring' has traversed (middle), and the actual force in piconewton measured with the 'spring' using Hooke's law (right side). The frames were drawn with MolScript v1.4 [Kraulis 1991] and Raster3D [Anderson et al. 1988].
The forth movie illustrates the unbinding process at low loading rates.
Journal of Applied Chrystallography (24) 946-950 (1991)