Role of the hydrophobic and hydrophilic sites in the dynamic crossover of the protein-hydration water

Abstract

h i g h l i g h t s• The water diffusion near the protein surface is lower than in bulk.• A crossover in the diffusion of the hydration water is observed.• The crossover happens at different temperatures for hydrophilic and hydrophobic sites. g r a p h i c a l a b s t r a c t a b s t r a c t Molecular dynamics simulations were performed to study the water structure and dynamics in the hydration shell of the globular TS-Kappa protein. The results show that for a wide range of temperatures the diffusion coefficient of water near the protein surface is lower than in bulk. A crossover in the diffusion behavior of hydration water is observed at different temperatures for hydrophilic and hydrophobic vicinities. We have found a correlation between the crossover in the hydrophilic case and the protein dynamical transition. An explanation in terms of the competition between water-water water-protein H-bond formation is provided based on H-bond network analysis.

The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

“…On the basis of this approach, for what concerns the thermal limit of biological activity, the low-temperature threshold, TL≃225 K, corresponds to what was originally named the protein glass transition, below which the hydrogen-bonded network becomes too rigid to allow protein motions and the whole system can be considered in a glassy state. It corresponds to the temperature of the so-called water dynamical crossover at which point the population of local low-density water structures dominates over that of high-density local structures [27,35,52,53,60,64,65]. This change in the water density and in the corresponding dynamics of the hydrogen-bonded network triggers the amino acids motion and the protein activity.…”

“…Since the water monolayer covering the protein surface is essentially a bidimensional hydrogen-bonded network connecting the different water clusters and the hydrophilic moieties of the protein surface [22,23], the protein dynamics, and thus its function, is slave to water dynamics [24,25,26]. Hence, the magnitude of the self-diffusion of hydration water strictly influences the large-amplitude motion of protein residues that is needed for the corresponding functionality [27,28].…”

Dynamical aspects of supercooled TIP3P–water in the grooves of DNA

“…Water in the vicinity of hydrophobic and hydrophilic sites of the protein exhibits a dynamical behavior which is quite distinct when compared to bulk water. [20][21][22][23][24][25][26][27] Recently, experiments and simulations with water at the GFP and CYP proteins showed that water molecules at the biomolecule surface present a very slow dynamics and they get stuck in some places, suggesting the presence of fractal traps on the protein surface. 28,29 In these systems, the water near the protein exhibits a subdiffusive behavior in which the mean squared displacement (MSD) of the molecules grows nonlinearly with time, i.e., ⟨r 2 (t)⟩∝ t µ , in which µ < 1 for subdiffusion.…”

2D nanoporous membrane for cation removal from water: Effects of ionic valence, membrane hydrophobicity, and pore size

“…Recent studies have shown that the water dynamics and structure inside hydrophobic or hydrophilic pores can be quite distinct regarding the pore size [28][29][30] and even near hydrophobic or hydrophilic protein sites. 31 Three cations are considered: the standard monovalent sodium (Na + ), the divalent zinc (Zn 2+ ), and the trivalent iron (Fe 3+ ). The study of sodium removal is relevant due to its applications for water desalination.…”