Microtubule circumferential vibrations in cytosol

Optomechanical proposal for monitoring microtubule mechanical vibrations

Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.

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

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 C_α 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.

FINITE ELEMENT ANALYSIS OF MECHANICAL DEFORMATION OF CHONDROCYTE TO 2D SUBSTRATE AND 3D SCAFFOLD

The mechanical properties of cells are important in regulation of many aspects of cell functions. The cell may respond differently to a 2D plate and a 3D scaffold. In this study, the finite element analysis (FEA) was adopted to investigate mechanical deformation of chondrocyte on a 2D glass plate and chondrocyte seeded in a 3D scaffold. The elastic properties of the cell differ in these two different compression tests. This is because that the cell sensed different environment (2D plate and 3D construct) which can alter its structure and mechanical properties. It reveals how the apparent Poisson's ratio of a cell changes with the applied strain depends on its mechanical environment (e.g., the elastic moduli and Poisson's ratios of the scaffold and extracellular matrix) which regulates cell mechanics. In addition, the elastic modulus of the nucleus also plays a significant role in the determination of the Poisson's ratio of the cell for the cells seeded scaffold. It also reveals the intrinsic Poisson's ratio of the cell cannot be obtained by extrapolating the measured apparent Poisson's ratio to zero strain, particularly when scaffold's Poisson's ratio is quite different from the cell.

Localized vibration of a microtubule surrounded by randomly distributed cross linkers

Based on finite element simulation, the present work studies free vibration of a microtubule surrounded by 3D randomly distributed cross linkers in living cells. A basic result of the present work is that transverse vibration modes associated with the lowest frequencies are highly localized, in sharp contrast to the through-length modes predicted by the commonly used classic elastic foundation model. Our simulations show that the deflected length of localized modes increases with increasing frequency and approaches the entire length of microtubule when frequency approaches the minimum classic frequency given by the elastic foundation model. In particular, unlike the length-sensitive classic frequencies predicted by the elastic foundation model, the lowest frequencies of localized modes predicted by the present model are insensitive to the length of microtubules and are at least 50% lower than the minimum classic frequency for infinitely long microtubules and could be one order of magnitude lower than the minimum classic frequency for shorter microtubules (only a few microns in length). These results suggest that the existing elastic foundation model may have overestimated the lowest frequencies of microtubules in vivo. Finally, based on our simulation results, some empirical relations are proposed for the critical (lowest) frequency of localized modes and the associated wave length. Compared to the classic elastic foundation model, the localized vibration modes and the associated wave lengths predicted by the present model are in better agreement with some known experimental observations.

A higher-order mathematical modeling for dynamic behavior of protein microtubule shell structures including shear deformation and small-scale effects

Microtubules in mammalian cells are cylindrical protein polymers which structurally and dynamically organize functional activities in living cells. They are important for maintaining cell structures, providing platforms for intracellular transport, and forming the spindle during mitosis, as well as other cellular processes. Various in vitro studies have shown that microtubules react to applied mechanical loading and physical environment. To investigate the mechanisms underlying such phenomena, a mathematical model based on the orthotropic higher-order shear deformation shell formulation and Hamilton's principle is presented in this paper for dynamic behavior of microtubules. The numerical results obtained by the proposed shell model are verified by the experimental data from the literature, showing great consistency. The nonlocal elasticity theory is also utilized to describe the nano-scale effects of the microtubule structure. The wave propagation and vibration characteristics of the microtubule are examined in the presence and absence of the cytosol employing proposed formulations. The effects of different system parameters such as length, small scale parameter, and cytosol viscosity on vibrational behavior of a microtubule are elucidated. The definitions of critical length and critical viscosity are introduced and the results obtained using the higher order shell model are compared with those obtained employing a first-order shear deformation theory. This comparison shows that the small scale effects become important for higher values of the wave vector and the proposed model gives more accurate results for both small and large values of wave vectors. Moreover, it is shown that for higher circumferential wave number, the torsional wave velocity obtained by the higher-order shell model tend to be higher than the one predicted by the first-order shell model.

FINITE ELEMENT MODELING OF THE THERMAL FLUCTUATIONS OF A SINGLE ANISOTROPIC POLYMER

Thermal fluctuations of microtubules (MTs) and other cytoskeletal filaments govern to a great extent the complex rheological properties of the cytoskeleton in eukaryotic cells. In recent years, much effort has been put into capturing the dynamics of these fluctuations by means of analytical and numerical models. These attempts have been very successful for, but also remain limited to, isotropic polymers. To correctly interpret experimental work on (strongly) anisotropic semiflexible polymers, there is a need for a numerical modeling tool that accurately captures the dynamics of polymers with anisotropic material properties. In the current study, we present a finite element (FE) framework for simulating the thermal dynamics of a single anisotropic semiflexible polymer. First, we demonstrated the accuracy of our framework by comparison of the simulated mean square displacement (MSD) of the end-to-end distance with analytical predictions based on the worm-like chain model. Then, we implemented a transversely isotropic material model, characteristic for biopolymers such as MTs, and studied the persistence length for various ratios between the longitudinal shear modulus, G12, and corresponding Young's modulus, E1. Finally, we put our findings in context by addressing a recent experimental work on grafted transversely isotropic MTs. In that research, a simplified static mechanical model was used to deduce a very high level of MT anisotropy to explain the observation that the persistence length of grafted MTs increases as contour length increases. We showed, by means of our FE framework, that the anisotropic properties cannot account for the reported length-dependent persistence length.