The dynamics of nanoscopic cavities holding a protein inside, and located in aqueous solution, is explored. The investigation centres on significant biomolecules as lysozyme and tenebrio molitor antifreeze protein. The inhibitor barstar is also taken into consideration. The cavities exhibit radii R ranging from 2.30 to 4.50 nm. With a resolution of femtoseconds, the progressive filling of those cavities with water molecules from the solvent has been monitored as a function of time. The creation of protein-water hydrogen bonds, to constitute the inner biomolecule hydration shell, has been followed at the nanoscale using all-atoms molecular dynamics simulations. The biological character of the water approximating the protein has been found to play a significant role in the solvation process of the biomolecules. In spite of the intrinsic differences between the proteins, due to their inherent nature, the dynamics of all those systems has been well described using the same model, a model of the author’s own which it has been named as cavity-protein two-state (CP2S) model. Likewise, the evolution of various physical magnitudes with the size of the cavity is found noticeably analogous for the different proteins under study. In like manner, the energy of the two level-system, associated to the CP2S model, is calculated to be of the order of some tens of THz, for all examined biomolecules. Comparison with experimental data is also supplied.

This work was supported by MCIN/AEI/10.13039/501100011033 [grant number PID2020-113582GB-I00], Spain, and the Government of Aragon, Spain, [grant number E36_23R, research group FENOL].

Peer reviewed