New Methods For Extracting Ultrafast Water Dynamics At Interfaces

Author : Yangzhong Qin
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (91 download)

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Download or read book Ultrafast Hydration Dynamics Probed by Tryptophan at Protein Surface and Protein-DNA Interface written by Yangzhong Qin and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: As we all live in a special water planet Earth, the significance of water to life has been universally recognized. The reason why water is so important to life has intrigued many researchers. This dissertation will focus on the ultrafast dynamics of protein surface water and protein-DNA interfacial water which have direct importance to the protein structure and function. Using tryptophan as an intrinsic fluorescence probe, combined with site-directed mutagenesis and ultrafast fluorescence up-conversion spectroscopy, we can achieve single residue spatial resolution and femtosecond temporal resolution. We can also precisely determine the local hydration water dynamics by monitoring the Stokes shift of tryptophan one at a time. Previously, the protein surface hydration has been extensively studied by our group. In this thesis, we will provide more details on the methods we are using to extract the hydration dynamics, and also validate our methods from both experimental and theoretical perspectives. To further interrogate the interfacial water hydration dynamics relative to the protein surface hydration, we studied two DNA polymerases: DNA Polymerase IV (Dpo4) and DNA Polymerase Beta (Pol ß). Both proteins show typical surface hydration pattern with three distinct time components including: (i) the ultrafast sub-picosecond component reflects the bulk type water motion; (ii) a few picoseconds component shows the inner water relaxation mainly corresponding to the local libration and reorientation; (iii) the tens to hundred picoseconds component represents the water-protein coupled motion involving the whole water network reorganization. Dpo4, a loosely DNA binding protein, exhibits very flexible interfacial water which resembles its surface water yet with a significantly reduced ultrafast component. Such dynamic interfacial water not only maintains interfacial flexibility, but also contributes to the low fidelity of the protein. In contrast to the Dpo4, pol ß tightly binds to the DNA with higher fidelity. The interfacial water is about 2 times slower than the surface water. Most importantly, the ultrafast component disappeared for the interfacial water indicating a strongly confined local environment. To further inspect the surface and interfacial water property, we carried out a 4 ns MD simulation, which reveals that all the interfacial water forms only one to two hydration layers from the protein and DNA surface, and no bulk type water was discovered. For both enzymes, the interfacial water is still fluctuating on picoseconds time scales to facilitate their dynamic function including substrate binding, protein sliding on DNA and dNTP sampling. Despite many hydration dynamics were studied at room temperature, some enzymes are optimally functioning at much higher temperature. Dpo4 was originally found on Sulfolobus solfataricus, which grows in volcanic hot springs with temperature around 75-90 °C. This inspired us to study its hydration temperature dependence from 1 °C to 60 °C. Simple Arrhenius equation can fit all the data for each mutant and determine the activation enthalpies ranging from 5 kJ/mol to 15 kJ/mol. We also found a clear correlation between the solvation and tryptophan side chain motion, strongly supporting the coupled motion between water and protein and the famous slaving model.