Abstract
The time-dependent Stokes shift (TDSS) has attracted increasing interest for measuring hydration dynamics around biomolecules during the last decades. Its ability to report on hydration dynamics around proteins, however, was questioned recently since the experimental signal stems from both water and protein motion with an unknown ratio of contribution. Using large-scale computer simulations, we examine the ability of the TDSS to capture local hydration dynamics at nine different sites around the protein ubiquitin. By computationally constraining protein motion, it is shown that the remaining water component is meaningful and in line with the picture of a heterogeneous yet overall mobile hydration layer. However, protein contributions are excessively large and cannot be removed in an experimental context, thus obscuring the water component. Consequently, we conclude that the experimental TDSS may not be suitable for the investigation of hydration dynamics around proteins.
Highlights
The dynamics of water in the vicinity of proteins and other biomolecules differs from bulk water dynamics
We investigate our system with respect to linear response theory (LRT), which is assumed to be applicable when inferring equilibrium properties from the nonequilibrium time-dependent Stokes shift (TDSS) experiment
Besides the total TDSS, which can be obtained experimentally, we provide a decomposition into water and protein contributions for each signal, as well as the TDSS from separate simulations, where protein motion is constrained, in order to assess the influence of protein–water coupling
Summary
The dynamics of water in the vicinity of proteins and other biomolecules differs from bulk water dynamics. Fluorescence spectroscopy uses a molecular probe to indirectly measure the collective relaxation of its surroundings. This probe can be a chromophore that is introduced into the system or one that is naturally present, e.g., tryptophan in proteins. The surroundings adapt to the altered electrostatic potential of the chromophore, lowering its emitted fluorescence frequencies. These time-dependent frequencies represent the relaxation of the surroundings in response to a change in the chromophore’s charge distribution
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