Mechanical behavior of actin and spectrin subjected to high strain rate: A molecular dynamics simulation study

Mechanical characterization of spectrin at the molecular level

Spectrin, a large cytoskeletal protein, consists of a heterodimeric structure comprising α and β subunits. Here, we have studied the mechanics of spectrin filament as a major constituent of dendrites and dendritic spines. Given the intricate biological details and compact biological construction of spectrin, we've developed a constitutive model of spectrin that describes its continuous deformation over three distinct stages and it's progressive failure mechanisms. Our model closely predicts both the force at which uncoiling begins and the ultimate force at which spectrin fails, measuring approximately 93 ~ 100 pN. Remarkably, our predicted failure force closely matches the findings from AFM experiments focused on the uncoiling of spectrin repeats, which reported a force of 90 pN. Our theoretical model proposes a plausible pathway for the potential failure of dendrites and the intricate connection between strain and strain rate. These findings deepen our understanding of how spectrin can contribute to traumatic brain injury risk analysis.

Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cell cortex

The cell cortex is a dynamic assembly formed by the plasma membrane and underlying cytoskeleton. As the main determinant of cell shape, the cortex ensures its integrity during passive and active deformations by adapting cytoskeleton topologies through yet poorly understood mechanisms. The spectrin meshwork ensures such adaptation in erythrocytes and neurons by adopting different organizations. Erythrocytes rely on triangular-like lattices of spectrin tetramers, whereas in neurons they are organized in parallel, periodic arrays. Since spectrin is ubiquitously expressed, we exploited Expansion Microscopy to discover that, in fibroblasts, distinct meshwork densities co-exist. Through biophysical measurements and computational modeling, we show that the non-polarized spectrin meshwork, with the intervention of actomyosin, can dynamically transition into polarized clusters fenced by actin stress fibers that resemble periodic arrays as found in neurons. Clusters experience lower mechanical stress and turnover, despite displaying an extension close to the tetramer contour length. Our study sheds light on the adaptive properties of spectrin, which participates in the protection of the cell cortex by varying its densities in response to key mechanical features.

Mechanical Responses of a Single Myelin Layer: A Molecular Simulation Study

The myelin sheath provides insulation to the brain's neuron cells, which aids in signal transmission and communication with the body. Degenerated myelin hampers the connection between the glial cells, which are the front row responders during traumatic brain injury mitigation. Thus, the structural integrity of the myelin layer is critical for protecting the brain tissue from traumatic injury. At the molecular level, myelin consists of a lipid bilayer, myelin basic proteins (MBP), proteolipid proteins (PLP), water and ions. Structurally, the myelin sheath is formed by repeatedly wrapping forty or more myelin layers around an axon. Here, we have used molecular dynamic simulations to model and capture the tensile response of a single myelin layer. An openly available molecular dynamic solver, LAMMPS, was used to conduct the simulations. The interatomic potentials for the interacting atoms and molecules were defined using CHARMM force fields. Following a standard equilibration process, the molecular model was stretched uniaxially at a deformation rate of 5 Å/ps. We observed that, at around 10% applied strain, the myelin started to cohesively fail via flaw formation inside the bilayers. Further stretching led to a continued expansion of the defect inside the bilayer, both radially and transversely. This study provides the cellular-level mechanisms of myelin damage due to mechanical load.

Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cortex

The cell cortex is a dynamic assembly that ensures cell integrity during passive deformation or active response by adapting cytoskeleton topologies with poorly understood mechanisms. The spectrin meshwork ensures such adaptation in erythrocytes and neurons. Erythrocytes rely on triangular-like lattices of spectrin tetramers, which in neurons are organized in periodic arrays. We exploited Expansion Microscopy to discover that these two distinct topologies can co-exist in other mammalian cells such as fibroblasts. We show through biophysical measurements and computational modeling that spectrin provides coverage of the cortex and, with the intervention of actomyosin, erythroid-like lattices can dynamically transition into condensates resembling neuron-like periodic arrays fenced by actin stress fibers. Spectrin condensates experience lower mechanical stress and turnover despite displaying an extension close to the contour length of the tetramer. Our study sheds light on the adaptive properties of spectrin, which ensures protection of the cortex by undergoing mechanically induced topological transitions.

Viscoelastic damage evaluation of the axon

In this manuscript, we have studied the microstructure of the axonal cytoskeleton and adopted a bottom-up approach to evaluate the mechanical responses of axons. The cytoskeleton of the axon includes the microtubules (MT), Tau proteins (Tau), neurofilaments (NF), and microfilaments (MF). Although most of the rigidity of the axons is due to the MT, the viscoelastic response of axons comes from the Tau. Early studies have shown that NF and MF do not provide significant elasticity to the overall response of axons. Therefore, the most critical aspect of the mechanical response of axons is the microstructural topology of how MT and Tau are connected and construct the cross-linked network. Using a scanning electron microscope (SEM), the cross-sectional view of the axons revealed that the MTs are organized in a hexagonal array and cross-linked by Tau. Therefore, we have developed a hexagonal Representative Volume Element (RVE) of the axonal microstructure with MT and Tau as fibers. The matrix of the RVE is modeled by considering a combined effect of NF and MF. A parametric study is done by varying fiber geometric and mechanical properties. The Young’s modulus and spacing of MT are varied between 1.5 and 1.9 GPa and 20–38 nm, respectively. Tau is modeled as a 3-parameter General Maxwell viscoelastic material. The failure strains for MT and Tau are taken to be 50 and 40%, respectively. A total of 4 RVEs are prepared for finite element analysis, and six loading cases are inspected to quantify the three-dimensional (3D) viscoelastic relaxation response. The volume-averaged stress and strain are then used to fit the relaxation Prony series. Next, we imposed varying strain rates (between 10/sec to 50/sec) on the RVE and analyzed the axonal failure process. We have observed that the 40% failure strain of Tau is achieved in all strain rates before the MT reaches its failure strain of 50%. The corresponding axonal failure strain and stress vary between 6 and 11% and 5–19.8 MPa, respectively. This study can be used to model macroscale axonal aggregate typical of the white matter region of the brain tissue.

Molecular and structural basis of actin filament severing by ADF/cofilin

ADF/cofilin’s cooperative binding to actin filament modifies the conformation and alignment of G-actin subunits locally, causing the filament to sever at “boundaries” formed among bare and ADF/cofilin-occupied regions. Analysis of the impact of the ADF/cofilin cluster boundary on the deformation behavior of actin filaments in a mechanically strained environment is critical for understanding the biophysics of their severing. The present investigation uses molecular dynamics simulations to generate atomic resolution models of bare, partially, and fully cofilin decorated actin filaments. Steered molecular dynamics simulations are utilized to determine the mechanical properties of three filament models when subjected to axial stretching, axial compression, and bending forces. We highlight differences in strain distribution, failure mechanisms in the three filament models, and biomechanical effects of cofilin cluster boundaries in overall filament rupture. Based on the influence of ADF/cofilin binding on intrastrand and interstrand G-actin interfaces, the cofilin-mediated actin filament severing model proposed here can help understand cofilin mediated actin dynamics.

Finite element analysis of the influence of cyclic strain on cells anchored to substrates with varying properties

The response of cytoskeleton to mechanical cues plays a pivotal role in understanding several aspects of cellular growth, migration, and cell-cell and cell-matrix interactions under normal and diseased conditions. Finite element analysis (FEA) has become a powerful computational technique to study the response of cytoskeleton in the maintenance of overall cellular mechanics. With the revelation of role of external mechanical microenvironment on cell mechanics, FEA models have also been developed to simulate the effect of substrate stiffness on the mechanical properties of cancer cells. However, the models developed so far model cellular response under static mode, whereas in physiological condition, cells always experience dynamic loading conditions. To develop a more accurate model of cell-extracellular matrix (ECM) interactions, this paper models the cytoskeleton and other parts of the cell by beam and solid elements respectively, assuming spherical morphology of the cell. The stiffness and roughness of extracellular matrix were varied. Furthermore, static and dynamic sinusoidal loads were applied through a flat plate indenter on the cell along with providing sinusoidal strain at the substrate. It is observed that due to axial loading, cell reaches a plastic region, and when the sinusoidal loading is added to the axial load, the cell experiences permanent deformation. Degradation of the cytoskeleton elements and a physiologically more relevant spherical cap shape of the cell were also considered during the analysis. This study suggests that asperity topology of the substrate and indirect cyclic load can play a significant role in the shape alterations and motion of a cell.

Effect of Strain Rate on Single Tau, Dimerized Tau and Tau-Microtubule Interface: A Molecular Dynamics Simulation Study

Microtubule-associated protein (MAP) tau is a cross-linking molecule that provides structural stability to axonal microtubules (MT). It is considered a potential biomarker for Alzheimer's disease (AD), dementia, and other neurological disorders. It is also a signature protein for Traumatic Brain Injury (TBI) assessment. In the case of TBI, extreme dynamic mechanical energies can be felt by the axonal cytoskeletal members. As such, fundamental understandings of the responses of single tau protein, polymerized tau protein, and tau-microtubule interfaces under high-rate mechanical forces are important. This study attempts to determine the high-strain rate mechanical behavior of single tau, dimerized tau, and tau-MT interface using molecular dynamics (MD) simulation. The results show that a single tau protein is a highly stretchable soft polymer. During deformation, first, it significantly unfolds against van der Waals and electrostatic bonds. Then it stretches against strong covalent bonds. We found that tau acts as a viscoelastic material, and its stiffness increases with the strain rate. The unfolding stiffness can be ~50-500 MPa, while pure stretching stiffness can be >2 GPa. The dimerized tau model exhibits similar behavior under similar strain rates, and tau sliding from another tau is not observed until it is stretched to >7 times of original length, depending on the strain rate. The tau-MT interface simulations show that very high strain and strain rates are required to separate tau from MT suggesting Tau-MT bonding is stronger than MT subunit bonding between themselves. The dimerized tau-MT interface simulations suggest that tau-tau bonding is stronger than tau-MT bonding. In summary, this study focuses on the structural response of individual cytoskeletal components, namely microtubule (MT) and tau protein. Furthermore, we consider not only the individual response of a component, but also their interaction with each other (such as tau with tau or tau with MT). This study will eventually pave the way to build a bottom-up multiscale brain model and analyze TBI more comprehensively.

The axonal radial contractility: Structural basis underlying a new form of neural plasticity

Axons are the longest cellular structure reaching over a meter in the case of human motor axons. They have a relatively small diameter and contain several cytoskeletal elements that mediate both material and information exchange within neurons. Recently, a novel type of axonal plasticity, termed axonal radial contractility, has been unveiled. It is represented by dynamic and transient diameter changes of the axon shaft to accommodate the passages of large organelles. Mechanisms underpinning this plasticity are not fully understood. Here, we first summarised recent evidence of the functional relevance for axon radial contractility, then discussed the underlying structural basis, reviewing nanoscopic evidence of the subtle changes. Two models are proposed to explain how actomyosin rings are organised. Possible roles of non-muscle myosin II (NM-II) in axon degeneration are discussed. Finally, we discuss the concept of periodic functional nanodomains, which could sense extracellular cues and coordinate the axonal responses. Also see the video abstract here: https://youtu.be/ojCnrJ8RCRc.