Mechanical transduction via a single soft polymer

Abstract

Molecular machines from biology and nanotechnology often depend on soft structures to perform mechanical functions, but the underlying mechanisms and advantages or disadvantages over rigid structures are not fully understood. We report here a rigorous study of mechanical transduction along a single soft polymer based on exact solutions to the realistic three-dimensional wormlike-chain model and augmented with analytical relations derived from simpler polymer models. The results reveal surprisingly that a soft polymer with vanishingly small persistence length below a single chemical bond still transduces biased displacement and mechanical work up to practically significant amounts. This "soft" approach possesses unique advantages over the conventional wisdom of rigidity-based transduction, and potentially leads to a unified mechanism for effective allosterylike transduction and relay of mechanical actions, information, control, and molecules from one position to another in molecular devices and motors. This study also identifies an entropy limit unique to the soft transduction, and thereby suggests a possibility of detecting higher efficiency for kinesin motor and mutants in future experiments.

Diffusion Biased by a Soft Neck Linker Regulates Kinesin Stepping

“…Our fitting is consistent with this predication. When a resisting load is imposed on the motor, the diffusion bias can be reduced or even reversed (eq ), which has been verified by the mechanical study (for details, see Figure 4 in ref ). According to eq , the load dependence of the diffusion bias is determined by the term of δ 23 + δ 25 = 0.5 with δ 25 being a small positive number (0.05 and 0.1 for fitting the data of refs and ; see Table ).…”

“…In the case of no loads, the diffusion process is constrained by the effect of neck linker zippering (Figure a). A predication suggested by a mechanical study, the neck linker zippering has the capability for transducing a diffusion bias exponentially proportional to ∼7 k B T (see Figure b). Our fitting is consistent with this predication.…”

“…The mechanical transition branches 2 → 3 and 2 → 5 correspond to the diffusion process of a tethered head, which determines the stepping direction (Figure a). A recent theory based on a wormlike chain model indicated that the diffusion of the detached head can be biased by the neck linker zippering . The diffusion bias for displacing the detached head to the forward site over the backward site can be quantified by an energy difference.…”

“…l c and l p correspond to the neck linker contour length and persistence length. (b) Diffusion bias exactly calculated based on a wormlike chain model with l c = 10 nm, l p = 0.5 nm, and θ = 0°; see details in ref .…”

“…The neck linker is a very soft peptide chain with a persistence length of less than 1 nm, whose mechanical capacity for a forward step is likely limited. A recent study , based on an exact solution of the wormlike chain model suggested that the forward bias induced by the neck linker zippering is approximately proportional to ∼7 k B T . The resisting force can reduce or even reverse the forward bias to regulate kinesin directional stepping.…”