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  • where is the breaking force In

    2024-04-02

    where is the breaking force. In the following, the details of the simulation are presented and subsequently, the results are discussed. The initial atomic structure is extracted from the crystal structure of single AF (PDB identification 3G37) which consist 12 monomers. As aforementioned 4 monomers are needed and hence, 4 monomers which are at the center of the filament are extracted from the structure. The simulation setup such as solvating, ionization and setting of the simulations are same as Section 3 expect those which are stated in the following. Both structures were minimized for 15,000 steps of a conjugate gradient in NAMD and equilibrated for 2 ns. In the SMD simulation, the spring constant was set to 10 kCal/mol/Å2 and the velocity was changed between 0.04 ps/Å and 1.0 ps/Å. Moreover, each simulation is performed three times for the sake of statics purposes and the obtained results are averaged. Fig. 11 shows the extracted F2mon and F4mon for the pulling velocity of 0.04 ps/Å during the simulation time. The red curve represents the case which two adjacent monomers are freely pulling in the solution. As depicted in the latter figure, when two monomers are pulled without any interaction by any other monomers (step 1) the force converged to a constant value, however for the case of 4 monomers, the curve of F4mon experiences a peak value and then converge to the F2mon. The differences between F4mon and F2mon is the result of the interaction among the monomers in the filament. When the forces reach its maximum value, the actin-actin bond breaks and allows the two monomers to be pulled. In the next step by subtracting the two curves of F4mon and F2mon, the breaking force is calculated and plotted in Fig. 12 for 5 different velocities. Moreover, Fig. 12 emphasizes the importance of the first step. As it is apparent from the latter figure, the breaking force converges to zero when the two monomers are separated completely. While the value of F4mon in the Fig. 11 converged to the F2mon. The results reveal that the breaking force is equal to 4197.5 pN which indicates the average of the 5 obtained values. It is also noteworthy that, Tsuda et al. (1996) reported the breaking force of actin-actin bond under torsion measured directly by in vitro micromanipulation. Their results are smaller from the present study (600-320 pN) which may be attributed to the torsion test and the variation in the filament length scales. Furthermore, Ghodsi and Kazemi (2012) simulated the elastic properties of (±)-Baclofen australia filament by applying a tension force to an actin trimer. Their extension forces are much greater than 600 pN which has been reported by Tsuda et al. (1996) and consequently, no rupture or breaking has been reported. Additionally, their tension force converged to values around  ∼ 5000 pN which may be a sign of breaking phenomena and is in good agreement with the present study. Of interest is that in Section 4.1 a model for the elastic properties of F-actin proposed. In that model, the bond between monomers assumed to be rigid. Now, comparing the elastic module of G-actin (both ATP and ADP states) shows that the actin-actin bond is stiffer than the monomer elastic properties which itself validate the assumption of the rigidity of the actin-actin bond in the model.
    Conclusion In our previous studies, we implemented experimental and computational techniques for analyzing cell cytoskeleton at varying conditions (Abeddoust, Shamloo, 2015, Shamloo, 2014, Shamloo, Manuchehrfar, Rafii-Tabar, 2015, Shamloo, Mohammadaliha, Mohseni, 2015). The main purpose of this paper was to draw attention to the nanomechanical behavior of the actin monomer. Actin is a semi-flexible polymer found as one of the main components of the cytoskeleton of cells. Generally, actin is involved in a static role in cell structure and a dynamic role in cell movement. The polymerization of actin can provide forces that drive the extension of cellular processes and movement of some organelles. In this paper, tensile stiffness of a single G-actin was investigated in both axial and lateral directions. Here, using steered molecular dynamics method, we carried out in silico tensile tests of a single actin monomer, monitoring the force-displacement response in the different direction of tensile load. Moreover, the effects of nucleotide binding pocket on the mechanical behavior of the actin monomer was studied. Based on the obtained results for the actin monomer, we proposed a simple structural model that describes actin filament as a hierarchical structure, providing a bottom-up description of elastic. The comparison of the obtained result and literature reveals that molecular dynamics simulation serves as a precise and sufficient approach in nanomechanics modeling. The findings presented here may thus be a step towards a better understanding of the mechanical properties of actin that lead to multiscale modelings. More precisely, proposing multiscale models needs the understanding of the mechanical properties of the building block which is investigated in the present study. However, viscoelastic modeling of G-actin can be investigated as a future work. As an example, in our F-actin model, the role/function of the helical conformation of the actin filament is not considered while it may be a good suggestion to develop the model and consider this phenomenon in both tensile and torsion modeling of the filament.