Delineating elastic properties of kinesin linker and their sensitivity to point mutations

TL;DR

This study uses steered molecular dynamics simulations and fluctuation relations to analyze the elastic properties of kinesin linker regions and how point mutations affect their mechanical behavior.

Contribution

It introduces a simulation-based approach to quantify the impact of specific amino acid mutations on kinesin linker elasticity and stability.

Findings

Asparagine and Lysine residues significantly influence linker stretching behavior.

Mutations to alanine alter the free energy landscape of the linker.

Simulation results highlight key residues controlling mechanical properties.

Abstract

We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The sample trajectories have been analyzed to derive distribution of work done on the system. In order to induce unfolding of the linker, we have stretched the molecule at a constant pulling force and allowed for a subsequent relaxation of its structure. The use of fluctuation relations (FR) relevant to non-equilibrium systems subject to thermal fluctuations allows us to assess the difference in free energy between stretched and relaxed conformations. To further understand effects of potential mutations on elastic properties of the linker, we have performed similar in silico studies on a structure formed of a polyalanine sequence (Ala-only) and on three other structures, created by substituting selected types of amino acid residues in the linker's sequence with alanine (Ala) ones. The results of SMD simulations indicate a crucial role played by the Asparagine (Asn) and Lysine (Lys) residues in controlling stretching and relaxation properties of the linker domain of the motor.