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Despite the widespread use of cancer chemotherapy drugs, the molecular mechanisms of action of many of them remain unclear. Some of these drugs, such as taxol, are known to affect the dynamics of microtubule assembly and stop the process of cell division in prophase-prometaphase. Recently, new spatial structures of microtubules and individual tubulin oligomers have emerged associated with various regulatory proteins and cancer chemotherapy drugs. However, knowledge of the spatial structure in itself does not provide information about the mechanism of action of drugs.

In this work, we applied the molecular dynamics method to study the behavior of taxol-bound tubulin oligomers and used our previously developed method for analyzing the conformation of tubulin protofilaments, based on the calculation of modified Euler angles. Recent structures of microtubule fragments have demonstrated that tubulin protofilaments bend not in the radial direction, as many researchers assume, but at an angle of approximately 45◦ from the radial direction. However, in the presence of taxol, the bending direction shifts closer to the radial direction. There was no significant difference between the mean bending and torsion angles of the studied tubulin structures when bound to the various natural regulatory ligands, guanosine triphosphate and guanosine diphosphate. The intra-dimer bending angle was found to be greater than the interdimer bending angle in all analyzed trajectories. This indicates that the bulk of the deformation energy is stored within the dimeric tubulin subunits and not between them. Analysis of the structures of the latest generation of tubulins indicated that the presence of taxol in the tubulin beta subunit pocket allosterically reduces the torsional rigidity of the tubulin oligomer, which could explain the underlying mechanism of taxol’s effect on microtubule dynamics. Indeed, a decrease in torsional rigidity makes it possible to maintain lateral connections between protofilaments, and therefore should lead to the stabilization of microtubules, which is what is observed in experiments. The results of the work shed light on the phenomenon of dynamic instability of microtubules and allow to come closer to understanding the molecular mechanisms of cell division.

Muscle contraction is controlled by Ca2+ ions via regulatory proteins, troponin and tropomyosin, associated with thin actin filaments in sarcomeres. Depending on the Ca2+ concentration, the thin filament rearranges so that tropomyosin moves along its surface, opening or closing access to actin for the motor domains of myosin molecules, and causing contraction or relaxation, respectively. Numerous point amino acid substitutions in tropomyosin are known, leading to genetic pathologies — myo- and cardiomyopathies caused by changes in the structural and functional properties of the thin filament. The results of molecular dynamics modeling of a fragment of a thin filament of cardiac muscle sarcomeres formed by fibrillar actin and wildtype tropomyosin or with amino acid substitutions: the double stabilizing substitution D137L/G126R and the cardiomyopathic substitution S215L are presented. For numerical calculations, we used a new model of a thin filament fragment containing 26 actin monomers and 4 tropomyosin dimers, with a refined structure of the region of overlap of neighboring tropomyosin molecules in each of the two tropomyosin strands. The simulation results showed that tropomyosin significantly increases the bending stiffness of the thin filament, as previously found experimentally. The double stabilizing replacement D137L/G126R leads to a further increase in this rigidity, and the replacement S215L, on the contrary, leads to its decrease, which also corresponds to experimental data. At the same time, these substitutions have different effects on the angular mobility of the actin helix and only slightly modulate the angular mobility of tropomyosin cables relative to the actin helix and the population of hydrogen bonds between negatively charged tropomyosin residues and positively charged actin residues. The results of the verification of the new model demonstrate that its quality is sufficient for the numerical study of the effect of single amino acid substitutions on the structure and dynamics of thin filaments and study the effects leading to dysregulation of muscle contraction. This model can be used as a useful tool for elucidating the molecular mechanisms of some genetic diseases and assessing the pathogenicity of newly discovered genetic variants.

The mechanical stability of cell adhesion protein Cadherin with explicit model of water is studied by the method of molecular dynamics. The protein in apo-form and with the ions of different types (Ca²⁺, Mg²⁺, Na⁺, K⁺) was unfolding with a constant speed by applying the force to the ends. Eight independent experiments were done for each form of the protein. It was shown that univalent ions stabilize the structure less than bivalent one under mechanical unfolding of the protein. A model system composed of two amino acids and the metal ion between them demonstrates properties similar to that of the cadherin in the stretching experiments. The systems with potassium and sodium ions have less mechanical stability then the systems with calcium and magnesium ions.