Deformation pattern in vibrating microtubule: Structural mechanics study based on an atomistic approach

Daniel Havelka,Michal Cifra,Marco A Deriu,Ondřej Kučera

doi:10.1038/s41598-017-04272-w

Abstract

The mechanical properties of microtubules are of great importance for understanding their biological function and for applications in artificial devices. Although microtubule mechanics has been extensively studied both theoretically and experimentally, the relation to its molecular structure is understood only partially. Here, we report on the structural analysis of microtubule vibration modes calculated by an atomistic approach. Molecular dynamics was applied to refine the atomic structure of a microtubule and a Cα elastic network model was analyzed for its normal modes. We mapped fluctuations and local deformations up to the level of individual aminoacid residues. The deformation is mode-shape dependent and principally different in α-tubulins and β-tubulins. Parts of the tubulin dimer sequence responding specifically to longitudinal and radial stress are identified. We show that substantial strain within a microtubule is located both in the regions of contact between adjacent dimers and in the body of tubulins. Our results provide supportive evidence for the generally accepted assumption that the mechanics of microtubules, including its anisotropy, is determined by the bonds between tubulins.

Highlights

To cope with all of their functions in eukaryotic cells, microtubules (MTs) evince extraordinary mechanical characteristics[1]
In accordance with previous studies, the vibration modes of microtubules of this length lie in the GHz range and the mode shapes can be roughly divided into four groups: stretching, bending, torsional, and breathing modes
We reported a high resolution analysis of the normal modes of a microtubule calculated by an atomistic approach, with special attention to the deformation of the microtubule body

Summary

Introduction

To cope with all of their functions in eukaryotic cells, microtubules (MTs) evince extraordinary mechanical characteristics[1]. We have identified explicit regions of αβ-tubulin atomic structure that undergo both high compression and extension depending on the mode of motion of the microtubule Since these regions are predominantly located at tubulin interfaces, it is evident that the mechanics of microtubules is dominated by bonds between tubulins instead of stiffness of tubulins themselves. This finding is of particular importance for (i) understanding the structural mechanics of microtubules on an intra-molecular level, and for (ii) prospective therapeutic targeting of microtubule mechanical properties, and for (iii) engineered modifications of microtubules in artificial applications

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