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Mechanical properties of a complete microtubule revealed through molecular dynamics simulation.

ABSTRACT: Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young's modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be investigated through computation. Typically, MD requires an atomic resolution structure of the molecule, which is unavailable for many systems, including MTs. By combining structural information from cryo-electron microscopy and electron crystallography, we have constructed an all-atom model of a complete MT and used MD to determine its mechanical properties. The simulations revealed nonlinear axial stress-strain behavior featuring a pronounced softening under extension, a possible plastic deformation transition under radial compression, and a distinct asymmetry in response to the two senses of twist. This work demonstrates the possibility of combining different levels of structural information to produce all-atom models suitable for quantitative MD simulations, which extends the range of systems amenable to the MD method and should enable exciting advances in our microscopic knowledge of biology.

SUBMITTER: Wells DB

PROVIDER: S-EPMC2905083 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature

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Mechanical properties of a complete microtubule revealed through molecular dynamics simulation.

Wells David B DB Aksimentiev Aleksei A

Biophysical journal 20100701 2

Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young's modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be ...[more]

PMID: 20643083

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Project description:The present study successfully implemented the ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism for the investigation of structural and dynamical properties of hydrated cobalt-porphyrin complexes. Considering the significance of cobalt ions in biological systems (for instance, vitamin B12), which reportedly incorporate cobalt ions in a d6, low spin, +3 state chelated in the corrin ring, an analog of porphyrin, the current study is focused on cobalt in the oxidation states +2 and +3 bound to the parent porphyrin lead structures embedded in an aqueous solution. These cobalt-porphyrin complexes were investigated in terms of their structural and dynamical properties at the quantum chemical level. The structural attributes of these hydrated complexes revealed the contrasting features of the water binding to these solutes, including a detailed evaluation of the associated dynamics. The study also yielded notable findings in regard to the respective electronic configurations vs coordination, which suggested that Co(II)-POR possesses a 5-fold square pyramidal coordination geometry in an aqueous solution containing the metal ion coordinating to four nitrogen atoms of the porphyrin ring and one axial water as the fifth ligand. On the other hand, high-spin Co(III)-POR was hypothesized to be more stable due to the smaller size-to-charge ratio of the cobalt ion, but the high-spin complex demonstrated unstable structural and dynamical behavior. However, the corresponding properties of the hydrated Co(III)LS-POR revealed a stable structure in an aqueous solution, thus suggesting the Co(III) ion to be in a low-spin state when bound to the porphyrin ring. Moreover, the structural and dynamical data were augmented by computing the free energy of water binding to the cobalt ions and the solvent-accessible surface area, which provide further information on thermochemical properties of the metal-water interaction and the hydrogen bonding potential of the porphyrin ring in these hydrated systems.

Dataset Information

Mechanical properties of a complete microtubule revealed through molecular dynamics simulation.

Publications

Mechanical properties of a complete microtubule revealed through molecular dynamics simulation.

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