Dynamic force spectroscopy is a valuable technique to explore the energy
landscape of molecular interactions. Polymer spacers are typically used to couple
the binding partners to the surfaces. To illustrate the impact of polymer spacers
on the measured rupture force and loading rate distributions we used a Monte
Carlo simulation, which was adjusted step by step towards realistic experimental
conditions. We found that the introduction of a polymer spacer with a
discrete length had only a marginal effect. However, a distribution of
polymer spacers with different lengths may induce drastic changes on the
distributions.
Three different methods for data analysis were then tested with regard to their
ability to reproduce the input values of the Monte Carlo simulations. We found
that simple linearization of all data points leads to an analysis error up to one
order of magnitude for the dissociation rate and one-third for the potential width.
The best results are achieved by determining the dissociation rate and the
potential width directly with a probability density function for the rupture forces
and the loading rates as a fit function that uses the dissociation rate and the
potential width as fit parameters. By applying this method the analysis errors
could be reduced below 25% for the dissociation rate and only 3% for the
potential width.
Applied to a set of experimental data this method proved to be extremely useful
and provided detailed information on the distributions. We are able to
discriminate specific and non-specific contributions of an aptamer–ligand
interaction and correct for the non-specific background. In addition, this
procedure allowed us to account for the low force instrumentation cut-off and
reconstruct the rupture force and force rate distributions.
The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.
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