ArticleBiophysical journal2010
Anisotropic elastic network modeling of entire microtubules.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Terahertz liquid networks: a mesoscopic passive architecture for circumventing physical deadlocks in brain-computer interfaces.Nanoscale advances · 2026Review
- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
- Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule.European biophysics journal : EBJ · 2021Article
- Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability.Biophysical journal · 2020Article
- Mechanics and kinetics of dynamic instability.eLife · 2020Article
- Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length.Frontiers in molecular biosciences · 2020Article
- When Stiffness Matters: Mechanosensing in Heart Development and Disease.Frontiers in cell and developmental biology · 2020Review
- Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability.PLoS computational biology · 2019Article
- Electromechanical vibration of microtubules and its application in biosensors.Journal of the Royal Society, Interface · 2019Article
- Article
- Structure-property relation and relevance of beam theories for microtubules: a coupled molecular and continuum mechanics study.Biomechanics and modeling in mechanobiology · 2018Article
- Computational modeling of single-cell mechanics and cytoskeletal mechanobiology.Wiley interdisciplinary reviews. Systems biology and medicine · 2018Review
- Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling.BMC structural biology · 2018Article
- TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid.Journal of physics. Condensed matter : an Institute of Physics journal · 2018Article
- Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies.Biophysical journal · 2018Article
- Explaining the Microtubule Energy Balance: Contributions Due to Dipole Moments, Charges, van der Waals and Solvation Energy.International journal of molecular sciences · 2017Article
- Deformation pattern in vibrating microtubule: Structural mechanics study based on an atomistic approach.Scientific reports · 2017Article
- Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics.Biology direct · 2017Article
- Radiofrequency and microwave interactions between biomolecular systems.Journal of biological physics · 2016Review
- Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.Biochemistry · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microtubules are supramolecular structures that make up the cytoskeleton and strongly affect the mechanical properties of the cell. Within the cytoskeleton filaments, the microtubule (MT) exhibits by far the highest bending stiffness. Bending stiffness depends on the mechanical properties and intermolecular interactions of the tubulin dimers (the MT building blocks). Computational molecular modeling has the potential for obtaining quantitative insights into this area. However, to our knowledge, standard molecular modeling techniques, such as molecular dynamics (MD) and normal mode analysis (NMA), are not yet able to simulate large molecular structures like the MTs; in fact, their possibilities are normally limited to much smaller protein complexes. In this work, we developed a multiscale approach by merging the modeling contribution from MD and NMA. In particular, MD simulations were used to refine the molecular conformation and arrangement of the tubulin dimers inside the MT lattice. Subsequently, NMA was used to investigate the vibrational properties of MTs modeled as an elastic network. The coarse-grain model here developed can describe systems of hundreds of interacting tubulin monomers (corresponding to up to 1,000,000 atoms). In particular, we were able to simulate coarse-grain models of entire MTs, with lengths up to 350 nm. A quantitative mechanical investigation was performed; from the bending and stretching modes, we estimated MT macroscopic properties such as bending stiffness, Young modulus, and persistence length, thus allowing a direct comparison with experimental data.
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