Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution

Abstract

Biological water at the interface of proteins is critical to their equilibrium structures and enzyme function and to phenomena such as molecular recognition and protein-protein interactions. To actually probe the dynamics of water structure at the surface, we must examine the protein itself, without disrupting the native structure, and the ultrafast elementary processes of hydration. Here we report direct study, with femtosecond resolution, of the dynamics of hydration at the surface of the enzyme protein Subtilisin Carlsberg, whose single Trp residue (Trp-113) was used as an intrinsic biological fluorescent probe. For the protein, we observed two well separated dynamical solvation times, 0.8 ps and 38 ps, whereas in bulk water, we obtained 180 fs and 1.1 ps. We also studied a covalently bonded probe at a separation of Ϸ7 Å and observed the near disappearance of the 38-ps component, with solvation being practically complete in (time constant) 1.5 ps. The degree of rigidity of the probe (anisotropy decay) and of the water environment (protein vs. micelle) was also studied. These results show that hydration at the surface is a dynamical process with two general types of trajectories, those that result from weak interactions with the selected surface site, giving rise to bulk-type solvation (Ϸ1 ps), and those that have a stronger interaction, enough to define a rigid water structure, with a solvation time of 38 ps, much slower than that of the bulk. At a distance of Ϸ7 Å from the surface, essentially all trajectories are bulk-type. The theoretical framework for these observations is discussed.W ater is essential for the stability and function of biological macromolecules, proteins and DNA. Hydration plays a major role in the assembly of a protein's structure and dynamics. For example, water molecules around hydrophobic and hydrophilic sites are important to the understanding of the activity of enzyme proteins (see, e.g., refs. 1-3) and are part of the recognition process by other molecules or proteins. The water molecules that make up the hydration shell in the immediate vicinity of the surface are particularly relevant to the function and, in that sense, are termed biological water; this distinction has been discussed clearly by Nandi and Bagchi (4) in relation to dielectric relaxations. The nature of this shell ''layer'' has been the focus of numerous studies both theoretically and experimentally (see refs. 5-12), yet there is no generalized picture of the dynamics at the local molecular level.X-ray crystallography, neutron diffraction, and molecular dynamics studies have shown (5-10) that at protein surfaces, water molecules are site-selective and can be restricted in their motion, even existing in the form of clusters in some cases. For example, neutron diffraction experiments (9) followed by molecular dynamics simulations on carboxymyoglobin (10) revealed that among the 89 water molecules associated with the protein, 4 remain bound during the entire length of the molecular dynamics simulation (50 ps), whereas ...

Protein hydration dynamics in solution: a critical survey

“…The validity of the linear response approximation in DSS studies has recently been questioned (BedardHearn et al 2003). Figure 7 shows DSS curves for tryptophan in water and in the protein subtilisin Carlsberg (Pal et al 2002b). Similar results have been reported for other proteins (Pal et al 2002c;Peon et al 2002).…”

“…The frequency shift caused by the difference in interactions with the environment between the ground and excited states, known as the Stokes shift, changes as the environment relaxes in . The bi-exponential curves are based on experimentally determined amplitudes and decay times (Pal et al 2002b). response to the altered charge distribution produced by electronic excitation. This evolution is described by the normalized DSS,…”

Hydrogen Bond Network of Water around Protein Investigated with Terahertz and Infrared Spectroscopy

“…Molecular dynamics (MD) simulations (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22) and other experimental approaches (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37) have revealed the protein is surrounded by dynamically retarded hydration water, with the innermost shell having a density higher than that of bulk water. However, even today, experimentally characterizing the dynamics and the structure of the water HB network in this hydration shell is challenging, because the water-water HB lifetime is very short (typically 1 ps) (38).…”

Hydrogen bond dynamics in aqueous NaBr solutions

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