Investigating the structural changes of myosin under high pressure processing by molecular dynamics simulations

Figures

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  Fig. 1. Conformational stability and structural dynamics of the myosin monomer under gradient HPP treatments. (a) Time-dependent root-mean-square deviation (RMSD) profiles of the protein backbone; (b) Residue-specific root-mean-square fluctuation (RMSF) values across the 922-residue monomeric chain; (c) Time-dependent radius of gyration (Rg) trajectories indicating global spatial extension; (d) Evolution of intramolecular hydrogen bond counts over the 100 ns production trajectories. Note: Simulations were performed under the NPT ensemble at a constant temperature of 298.15 K under four hydrostatic pressure conditions: 100KPa (cyan), 150 MPa (blue), 300 MPa (orange), and 450 MPa (red). Intramolecular hydrogen bonds in (d) were identified using CPPTRAJ based on standard geometric criteria (donor–acceptor distance ≤ 3.5 Å and donor–hydrogen–acceptor angle ≥ 120°).

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  Fig. 2. Free energy landscapes (FEL) of the myosin monomer under gradient HPP treatments. 2D projection and corresponding 3D surface representation of the relative free energy (G, in kcal/mol) profiles at (a) 100KPa, (b) 150 MPa, (c) 300 MPa, and (d) 450 MPa. Note: Free energy landscapes were constructed using backbone RMSD (relative to the minimized starting structure) and the Radius of Gyration (Rg) as the collective variables (CVs). The 2D joint probability distribution P(RMSD, Rg) was calculated via Kernel Density Estimation (KDE) with a Gaussian kernel applied to trajectory frames sampled every 10 ps. Relative free energy was calculated using the Boltzmann relation G = −kBTln[P/Pmax] at T = 298.15 K, where the lowest-energy conformation (dark blue basin) is defined as G = 0 kcal/mol.

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  Fig. 3. Interfacial compaction and morphological remodeling of the myosin motor domain contact model under gradient HPP treatments. (a) Time-dependent root-mean-square deviation (RMSD) profiles of the conplex backbone; (b) Time-dependent radius of gyration (Rg) trajectories of the overall contact model; (c) Solvent-accessible surface area (SASA) profiles of the model complex over the 100 ns simulation timescale. Note: Compressive simulations of the pre-aggregation intermediate (comprising two adjacent motor domains, residues 1–1844) were conducted at 100KPa (cyan), 150 MPa (blue), 300 MPa (orange), and 450 MPa (red). SASA values in (c) represent the total solvent-exposed surface area of the dimer complex, computed using a water probe radius of 1.4 Å.

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  Fig. 4. Thermodynamic, energetic, and interfacial residue-level characterization of the myosin contact-model interface under HPP. (a) Total system hydrogen bonds (intramolecular plus inter-subunit); (b) Number of active interfacial residue pairs across the Chain A–Chain B interface; (c) Symmetric 1844×1844 residue–residue distance contact maps averaged over the equilibrated trajectories; (d) Total number of interfacial hydrophobic contacts; (e) Estimated binding free energies (ΔGbind, in kcal/mol) calculated via MM-GBSA; (f) Energetic components of the binding affinity including van der Waals (VDWAALS), electrostatic (EEL), 1-4 electrostatic (1-4 EEL), polar solvation (EGB), and non-polar solvation (ESURF) terms. Note: Statistical analyses in (a), (b) and (d) were performed on n = 11 representative frames sampled at 10 ns intervals (including the equilibrated starting time) across the 100 ns production trajectories, and are reported as mean ± standard deviation (SD). Hydrophobic contacts in (d) and interfacial residues in (b) were identified using the nativecontacts command with a heavy-atom distance cutoff of 4.5 Å. In (c), distance maps represent the symmetric residue distance matrix,…

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  Fig. 5. Free energy landscapes (FEL) of the myosin motor domain contact model under gradient HPP treatments. 2D projection and corresponding 3D surface representation of the relative free energy (G, in kcal/mol) profiles of the contact model at (a) 100KPa, (b) 150 MPa, (c) 300 MPa, and (d) 450 MPa. Note: Landscapes were constructed using dimer backbone RMSD and the overall Radius of Gyration (Rg) as the collective variables (CVs). The 2D probability density and Boltzmann-derived relative free energy (G) were mapped using identical methodology and sampling parameters as described in Fig. 2.