Water in Biology |DNA Electron Transport Dynamics |
Macromolecular Recognition

Water in Biology*

Biological macromolecules—proteins and DNA—are physiologically inactive without water. While many aspects of structure and dynamics of bulk water can be regarded as reasonably understood at present, the same is not true for the water which is found in interfacial or restricted environments, such as the surface of proteins or micelles. Water at the surface of a protein defines a molecular layer that has been termed "biological water" and exhibits unique characteristics. The structure and dynamics of such layers, which are determined by the hydrophobic and hydrophilic interactions with the residues exposed to the water in the folded state, are important for the stability of proteins as well as for the mechanisms of protein-protein and protein-ligand association. For example, the energetics and dynamics of water desolvation have been suggested to be a determining factor in the process of protein-ligand recognition. In molecular dynamics simulations, water molecules have been found to mediate or bridge the interaction between DNA and proteins through their hydrogen bonding.

Upon femtosecond excitation of a probe localized at the surface of the biomolecule, an instant dipole is created. Water molecules, which can be visualized as tiny dipoles themselves, must respond to this instantaneously-established dipole moment, and bring the solvated macromolecule to a new equilibrated state.

Time-resolved fluorescence studies provide very detailed experimental information about the dynamics of solvation. In particular, with the time resolution of the fluorescence frequency up-conversion method, it has been possible to monitor solvation dynamics by following the evolution of the emission spectrum of a chromophore in solution on the timescale in which solvent relaxation occurs. The shift in the chromophore's emission frequency (peak), which accompanies the solvent relaxation, is then a measure of the dynamics of solvation. This method has been successfully applied to diverse systems ranging from the interfacial binding sites of enzymes to the major and minor grooves of DNA.

The femtosecond time resolution provides us with the opportunity of mapping out hydration dynamics on the time scale of the actual molecular motions of water. By constructing the hydration correlation function, which represents the solvent energy fluctuation, we obtain the fundamental time constants for solvation: ultrafast ~1 ps for free/quasi-free water molecules and tens of ps for bound water in the hydration layer, respectively.

Our theoretical studies of hydration relate our observations of solvation to the residence times on the protein surface and address the influence of dielectric relaxations, by rotational and translational motions, on the dynamics of bound-to-free water exchange. The latter is critical in view of the fact that the radial distribution function shows a manifestation of structured layer and MD simulations show the equilibration between bound and free molecules.

Hydration of proteins through weak forces is a dynamical process which defines a molecular layer on the scale of a few angstroms. The picosecond timescale of the dynamics excludes a static iceberg type model and it is clear that such ultrafast mobility, by rotational and translational motions, are unique in determining the hydrogen-bonded layer ordering and, hence, the structure and function. For the structure, the hydrophobic collapse in the interior of the protein and the hydrophilic interaction with hydrogen bonded water results in entropic and enthalpic changes which are determinants of the net free energy of stability. The hydrophilic structure in the protein exterior defines the order of the layer.

But the water in the layer has a finite residence time and its dynamics is an integral part of many functions: selective molecular recognition of ligands (substrate) through the unique directionality and adaptability of the hydrogen bond and water motion; enzymatic activity mediated by water located at the molecular distance scale, not diffusive; and protein-protein association through water mediation by entropic water displacement (desolvation) and energetic minimization of charge repulsion. With this in mind, the time scale for the dynamics is critical—it must be longer than bulk dynamics and shorter than the time for any unfolding of the active structure. To maintain selectivity and order in the layer, the picosecond timescale is ideal. For example, in protein-protein association, the timescale of translational diffusion is ~5 x 10-8 s while, as shown in our studies, the residence time is 4 orders of magnitude shorter, allowing for a very effective desolvation and search for the ideal configuration.

These studies promise many new extensions since femtosecond time resolution is ideal for such mapping of hydration, spatially and temporally.

*The text above has been adapted from the following publications.

Selected Publications

Dynamics of Ordered Water in Interfacial Enzyme Recognition: Bovine Pancreatic Phospholipase A2, L. Zhao, S. K. Pal, T. Xia, A. H. Zewail, Angew. Chem., Int. Ed. 2004, 43, 60.


Dynamics of Water in Biological Recognition, S. K. Pal A. H. Zewail, Chem. Rev. 2004, 104, 2099.

Dynamics of Ordered Water in Interfacial Enzyme Recognition: Bovine Pancreatic Phospholipase A2
, L. Zhao, S. K. Pal, T. Xia, A. H. Zewail, Angew. Chem., Int. Ed. 2004, 43, 60.

Site- and Sequence-Selective Ultrafast Hydration of DNA
, S. K. Pal, L. Zhao, T. Xia, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2003, 100, 13746.

Ultrafast Hydration Dynamics in Protein Unfolding: Human Serum Albumin, J. K. A. Kamal, L. Zhao, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2002, 101, 13411.

Biological Water: Femtosecond Dynamics of Macromolecular Hydration, S. K. Pal, J. Peon, B. Bagchi, A. H. Zewail, J. Phys. Chem. B 2002, 106, 12376.

Hydration at the Surface of the Protein Monellin: Dynamics with Femtosecond Resolution, J. Peon, S. K. Pal, A. H. Zewail, Proc. Natl. Acad. Sci. USA 2002, 99, 10964.