Open AccessDependence of Work on the Pulling Speed in Mechanical Ligand Unbinding
Author(s) -
Hong An Pham,
Duc Toan Truong,
Mai Suan Li
Publication year - 2021
Publication title -
the journal of physical chemistry. b
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.864
H-Index - 392
eISSN - 1520-6106
pISSN - 1520-5207
DOI - 10.1021/acs.jpcb.1c01818
Subject(s) - biomolecule , force spectroscopy , universality (dynamical systems) , work (physics) , ligand (biochemistry) , chemistry , molecule , molecular dynamics , chemical physics , physics , nanotechnology , thermodynamics , computational chemistry , materials science , quantum mechanics , receptor , biochemistry , organic chemistry
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 ∼ 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 ∼ 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.