Dynamics of water around a protein-DNA complex

Analysis of a large number of protein-DNA eomplexes leads to the following quantifieation of the above elassilieation. Only about 5-10% of surrounding water molecules belong to class (i) and 70-80% belong to class (ii). The rest belong to classes (iii) and (iv) [3], 

For example, in the trp repressor-DNA complex there are only a few direct contacts between the protein and the base-pairs [6]. It is interesting to note here that three ordered water molecules are found at the protein-DNA interface that are hydrogen-bonded with both the base pairs and the protein side-chain atoms. These water-mediated bases are among the most important parts in controlling the repressor s affinity for the operator sequence in the DNA. 

As discussed earlier, the usual ultrafast dynamics of water can become relatively slower in confined systems (such as reverse micelles and nanotubes) and also on interacting surfaces such as silica, protein surfaces, and in the grooves of DNA. Among different experimental methods, NMR techniques are more sensitive to the residence times of interior water molecules within internal polar cavities than to the surface water. Surface water molecules are rarely detected in NMR as they are in fast exchange with the bulk solvent, having residence times less than 500 ps. Interior 

Formation of a stable protein-DNA complex involves the rearrangement of water molecules and release of counter ions and water molecules to the bulk. Zewail and co-workers have used the time-resolved fluorescence up-conversion technique to explore the dynamics of the histone-DNA complex formation and the participation of hydration water in the stability and specificity of the recognition process [9]. This important study established the contribution from the entropic gain due to the release of hydration water (often termed dynamically ordered water) to the bulk. 

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