Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 125, Issue 30, Pages 8325-8330Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.1c01818
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Funding
- Narodowe Centrum Nauki in Poland [2019/35/B/ST4/02086]
- Department of Science and Technology at Ho Chi Minh City [07/2019/HD.-KHCNTT]
- TASK Supercomputer Center in Gdansk
- PLGrid Infrastructure, Poland
- ICST Computer Center, Ho Chi Minh City, Vietnam
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The paper investigates the relationship between non-equilibrium work and pulling speed in single-molecule force spectroscopy, showing a quadratic dependence of work on ln(V) and ln(2)(V) in the linear regime. This theory was confirmed through molecular dynamics simulations of protein-ligand complexes, indicating its applicability to various processes in biomolecular mechanics.
In single-molecule force spectroscopy, the rupture force F-max required for mechanical unfolding of a biomolecule or for pulling a ligand out of a binding site depends on the pulling speed V and, in the linear Bell-Evans regime, F-max similar to ln(V). Recently, it has been found that non-equilibrium work W is better than F-max in describing relative ligand binding affinity, but the dependence of W on V remains unknown. In this paper, we developed an analytical theory showing that in the linear regime, W similar to c(1) ln(V) + c(2) ln(2)(V), where c(1) and c(2) are constants. This quadratic dependence was also confirmed by all-atom steered molecular dynamics simulations of protein-ligand complexes. Although our theory was developed for ligand unbinding, it is also applicable to other processes, such as mechanical unfolding of proteins and other biomolecules, due to its universality.
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