protein hydration dynamics
Enzymes do not function without water. When we talk about the structure and dynamics of biomolecules, we almost always mean the hydrated form the molecule. Thanks to new experimental probes available in recent years, we have new data available on the dynamics of water near proteins and nucleic acids. The task is now to understand what this data is telling us about the interaction between biomolecules and their solvent environment. We have analyzed one experimental probe, the time-dependent Stokes shift, the shift in frequency between a photon that is absorbed and a photon that is subsequently emitted.
The photo-excited molecule has a different charge distribution than the ground state. The altered charged distribution perturbs the system, and the time-dependent Stokes shift gives us indirect information on the response of the water and biomolecule as they adjust to the altered charge distribution of the photo-excited system.
Much as been written about the layer of water surrounding a protein. Some have speculated that it is far different from ordinary water, and have even coined the term, "biological water". There has been a lively debate as to whether the Stokes shift gives information on protein motions, water motions, or both. Our analysis of the situation is found in the articles cited below.
- Ali Hassanali, Tanping Li, Dongping Zhong and Sherwin J. Singer,``Lys-trp-lys: Structure and dynamics in solution following photoexcitation'', J. Phys. Chem. B110(21):10497 (2006).
- Tanping Li, Ali A. Hassanali, Ya-Ting Kao, Dongping Zhong and Sherwin J. Singer, ``Hydration dynamics and time scales of coupled water-protein fluctuations'', J. Amer. Chem. Soc. 129(11):3376 (2007).
- Tanping Li, Ali A. Hassanali, Sherwin J. Singer, ``The origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer'', J. Phys. Chem. 112(50):16121 (2008).