QUANTIFICATION OF MOLECULAR BONDING

Higher organisms rely on mineral-polymer interactions for their skeletal structures and anchoring to their habitat. Medical and technological applications such as nanoparticles for ingestion and bioinspired and responsive materials are built on mineral-polymer interactions. However, the mechanistic understanding of these interactions is poorly constrained. Dynamic force spectroscopy (DFS) can probe the free energy landscape of interacting bonds and provide the underlying mechanistic information. However, obtaining qualitative thermodynamic and kinetic parameters from Polymer-linked DFS, has proven troublesome and erroneous data are currently being presented in the literature. 

 

We have developed a protocol for obtaining quantitative insight into polymer-mineral binding. We used theoretical calculations to prove the appropriate protocol of data analysis and demonstrate the approach by analyzing DFS data for literature and newly obtained data on mineral binding by biopolymers in microbial systems. Beside restating an appropriate method to tackle analyses of DFS data we have addressed 3 common difficulties’ in the DFS analyses:

dfs POLYMER.jpg

- determining the amount of bonds interacting 

- addressing the non-linear dependence of extension on applied force for biopolymers

- how to approach the overlooked equilibrium regime for polymer-based force spectroscopy

 

Our findings provide new insights into (bio)polymer-mineral interactions and both the conclusions and the approach are directly applicable to a broad range of disciplines, ranging from intracellular biomineralization to design of bioinspired functional materials for technologies, such as development of nanoparticles for biomedical applications.

https://www.nature.com/articles/s41598-017-09041-3

a) Schematic of DNA fixed to an AFM probe (in reality more molecules will be clustered at the probe. b) Energy landscape of a bond. The energy well defines the bound state at a distance xt away from the transition state. The energy difference between the bound and the transition state is ΔGbu. The intrinsic rate of unbinding, koff, describes the speed at which the unbinding occurs without an applied external force. c) The force spectrum can be divided in two regions: the near equilibrium regime and the kinetic regime where a bond breaks faster than it reforms. The intercept between the plateau of rupture forces in the near equilibrium regime and the y-axis defines the feq, the slope of the kinetic regime defines the xt and the intercept between a tangent of the kinetic regime and the x-axis defines the koff.

© 2019 by Karina K. Sand

karina.sand@gmail.com

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