High hydrostatic pressure can alter protein structure through changes in system volume, hydration, packing, and conformational sampling. We combined a sequential pressure and pressure-cooling molecular-dynamics pathway for tobacco mosaic virus coat protein (TMVcp) with replicate-resolved analysis of Native (1 bar, 300 K), high hydrostatic pressure (HHP; 2500 bar, 300 K), and HHP plus low temperature (HHP+LT; 2500 bar, 255 K). Three independently velocity-initialised 20 ns replicates were analysed per condition after discarding the first 200 ps, yielding 89,109 frames. Relative to Native, mean box volume decreased by 9.15% under HHP and 11.49% under HHP+LT, while density increased by 10.07% and 12.98%. Water occupancy within 0.35 nm increased by 10.73% and 18.45%, respectively; after normalization for bulk densification, the residual increase was near-null for HHP (+0.6%) but persisted for HHP+LT (+4.9%). In pooled Cartesian PCA, PC1-PC2 captured 38.5% of total variance but did not separate same-condition from across-condition replicate pairs (Jensen-Shannon divergence 0.771 versus 0.768; p = 0.476). Condition-associated signal instead concentrated in PC3-PC4, with mean divergence of 0.545 within conditions and 0.773 across conditions; selection-aware exact permutation retained significance (p = 0.0143). Pairwise C-alpha RMSD and backbone-dihedral PCA supported condition-associated differences, although first-half versus second-half divergences indicated incomplete convergence. Endpoint epitope comparisons showed residue-level enrichment for Native and HHP+LT, but not HHP. Overall, TMVcp exhibited robust volumetric responses, condition-dependent near-protein hydration, and reproducible but non-dominant conformational redistribution without implying equilibrium convergence or causal antibody remodelling. These findings distinguish pressure-driven densification from cooling-associated local hydration effects while preserving appropriate mechanistic caution.
Molecular dynamics of the α-helical hairpin structural motifs in five selected globular proteins were considered. The dynamics of each polypeptide chain were investigated on four independent trajectories with total time of 400 ns. A decrease in the dynamic mobility of α-helical hairpins was clearly observed in the regions containing certain amino acid residues. And that phenomena depends on the contacts of non-polar atoms of the hairpin residues with the other surrounding residues. This was demonstrated for α-helical hairpin motif but may also be applicable to the other structural motifs of the protein molecules. As a result, it is possible to estimate the dynamic behavior of any protein in aqueous solution and even predict structural changes of the polypeptide chain.
