1. Protein hydration shell formation: Dynamics of water in biological systems exhibiting nanoscopic cavities
- Author
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M.C. Morón, European Commission, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), and Gobierno de Aragón
- Subjects
Materials science ,02 engineering and technology ,Bulk water dynamics ,Nanoscopic cavities in water solutions ,010402 general chemistry ,01 natural sciences ,Protein hydration shell formation ,Molecular dynamics ,Materials Chemistry ,Molecule ,Physical and Theoretical Chemistry ,Two states model ,Nanoscopic scale ,Spectroscopy ,chemistry.chemical_classification ,Aqueous solution ,Hydrogen bond ,Biomolecule ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Solvation shell ,chemistry ,Chemical physics ,Radius of gyration ,Hydrogen bond network ,All-atoms molecular dynamics simulations ,0210 nano-technology - Abstract
This work explores the singular scenarios emerging from nanoscopic cavities, located in aqueous solutions, that include biomolecules and, as a consequence, the process of biomolecule hydration shell formation. The research presents a nano-scale study, performed in various systems related with protein-water solutions, using all-atoms molecular dynamics simulations. This research shows that if a protein falls within an empty nanoscopic cavity located in an aqueous solution, it will take a time, with a magnitude significant for biological processes, to rebuild its whole network of hydrogen bonds with the solvent molecules. During that protein isolation time the dynamics of the biomolecule, and therefore the corresponding bioactivity, will be seriously compromised. In the case of the protein barstar (radius of gyration of 1.17 nm) located in the centre of cavities with radius r from 2.5 to 4.5 nm, and solvent diffusion coefficients for bulk and physiologic water (2.4 and 1.5 μm2/ms, respectively), that time is found to be of the order of tens-hundreds of picoseconds, a significant temporal range concerning the dynamics and bioactivity of proteins. On the other hand, the dynamics of formation of the inner protein hydration shell has been followed using an atomic view. The required time has been found to decrease with r, as the network of water molecules approaching the biomolecule resembles that of the biological water corresponding to that biomolecule. That resemblance increases as those water molecules have previously been in close contact with the protein. The dynamics of those systems has been modelled using a two states model. Isolated bulk water is taken as reference for the computer simulations. Comparison with experimental data is also provided., This work was funded by the European Regional Development Fund (EU) together with the Government of Spain, under common Project FIS2017-87519-P. Financial support from the Government of Aragón (Aragón Research Group ‘Fenol’, E36_20R, Spain) and the European Union (Feder 2014-2020, Building Europe from Aragón) is also acknowledged.
- Published
- 2021