Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

Abstract

Kinesin walks processively on microtubules (MTs) in an asymmetric hand-over-hand manner consuming one ATP molecule per 16-nm step. The individual contributions due to docking of the approximately 13-residue neck linker to the leading head (deemed to be the power stroke) and diffusion of the trailing head (TH) that contributes in propelling the motor by 16 nm have not been quantified. We use molecular simulations by creating a coarse-grained model of the MT-kinesin complex, which reproduces the measured stall force as well as the force required to dislodge the motor head from the MT, to show that nearly three-quarters of the step occurs by bidirectional stochastic motion of the TH. However, docking of the neck linker to the leading head constrains the extent of diffusion and minimizes the probability that kinesin takes side steps, implying that both the events are necessary in the motility of kinesin and for the maintenance of processivity. Surprisingly, we find that during a single step, the TH stochastically hops multiple times between the geometrically accessible neighboring sites on the MT before forming a stable interaction with the target binding site with correct orientation between the motor head and the [Formula: see text] tubulin dimer.

Influenza as a molecular walker

“…27 The natural motor enzymes use ATP as fuel, whereas synthetic systems have a wider array of possible energy sources. 28,29 The rst molecular walker used DNA strands as fuel, quickly followed by an example that used ATP as fuel. 23,30 Instead of using the consumption of a chemical fuel to impose a strict directionality in each individual step, overall directionality can be attained when the direction of the steps is biased, for example using an enzyme with a chiral preference to cleave the back leg.…”

Mouse embryo geometry drives formation of robust signaling gradients through receptor localization

“…Receptor localization facilitates the formation of signaling gradient. To understand how receptor localization impacts BMP signaling between the ExE and epiblast, we simulated the movement of individual BMP4 ligands in the early mouse embryo (E6.0-E6.5) from secretion to receptor binding, using Brownian dynamics 27 . Given the evidence of polarized ligand secretion by epithelial cells in vitro 20,21 ( Supplementary Fig.…”

“…After secretion, BMP4 ligand diffusion is simulated as a random walk following Brownian dynamics. Ligand positions are updated after each time step h according to the equationr i t þ h ð Þ¼r i t ð Þ þΓ i t ð Þ, wherer i t ð Þ is the position of ligand i at time t.Γ i t ð Þis a random Brownian force acting on ligand i that satisfies constraints Γ i t ð Þ ¼ 0 andΓ i t ð ÞΓ j t′ ð Þ ¼ cDhδ ij δ tt′ , where D is the diffusion coefficient and c = 4 for 2D simulations or c = 6 for 3D simulations 27 . We estimate D = 20 μm 2 /s by default based on diffusion measurements of BMP homolog Dpp in the larval wing disc of Drosophila melanogaster 18 .…”

Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor–microtubule interaction strength

“…(ii) The reach of the unbound motor head (post-ATP binding and hydrolysis; state 4 or 4′ in Fig. 6) is determined by the interaction of the neck linker with the motor domain (49,50). For example, partial or complete necklinker docking in the 2HB conformation (while waiting for ATP; state 2) can potentially restrict the actual reach of the motor head during the diffusive search for the next tubulin binding site (post-ATP binding and hydrolysis; states 3 and 4).…”