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

Michał Świątek,Ewa Gudowska-Nowak

doi:10.1038/s41598-020-61399-z

Michał Świątek, Ewa Gudowska-Nowak

Open Access

https://doi.org/10.1038/s41598-020-61399-z

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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 stretching of the linker, we have applied a constant pulling force to the molecule 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.

Highlights

We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor
While its exact length as well as the placement within sequence of its N- and C- termini are not set in stone[9], some of its residue patterns are present across all kinesin families, while neck linker sequences within a single family are very similar[8]
In the initial part of our studies we have identified dynamic domains in the structure of Kinesin Heavy Chain (taken from PDB Databank(id:3kin)19) and analyzed deformations which have been obtained with a simplified mechanical model proposed by Hinsen[20]

Summary

Introduction

We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. Employing the methods of Molecular Dynamics and Normal Mode Analysis (NMA), we intend to deliver a more comprehensive description of a possible relation between neck linker’s amino acid sequence and the specificity of its function. A number of theoretical considerations are discussed, pertaining to thermodynamic description of an amino acid chain, ability to determine its elasticity via the force-extension relations and significance of non-equilibrium dynamics as used in our simulations. All these are placed in subsections of their own. The last section, \Conclusions, contains our closing remarks in which we summarise findings and highlight points of interest for future research in this field

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Conclusion