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Ultrafast Hydration Dynamics on Protein Surface and at Protein-DNA Interface

Yang, Yi
http://rave.ohiolink.edu/etdc/view?acc_num=osu1261450640

Abstract Details

2009, Doctor of Philosophy, Ohio State University, Physics.
Protein hydration dynamics are of fundamental importance to a protein’s structure and function as well as its recognition and interaction with substrates. Here, we present our studies of the ultrafast hydration dynamics on the protein surface of apomyoglobin (apoMb) and at protein-DNA interfaces of Polymerase β (Pol β) and DNA polymerase IV (Dpo4). The natural fluorescent amino acid tryptophan was applied as a local optical probe to detect environmental response using the femtosecond-resolved fluorescence up-conversion technique and reveal the hydration dynamics around proteins. With site-directed mutagenesis, tryptophan was placed at desired positions to investigate hydration dynamics on protein surfaces and interfaces in protein-DNA complexes with single-residue resolution. Sixteen single-tryptophan-containing mutants of apoMb were studied to map the global hydration dynamics around the protein surface in both the native and molten globule states. Two distinct hydration components are observed on time scales of a few (1-8 ps) and tens to hundreds of picoseconds (20-200 ps), reflecting the initial collective water relaxation and subsequent hydrogen-bond networking restructuring, respectively, and both time scales are strongly correlated with protein’s local structures and chemical properties. For Pol β, tryptophan was introduced one at a time at different positions around the surface of DNA binding pocket to map the water motions at the interface of the complex. Totally, twelve mutants were examined and a bimodal distribution of time scales for the water-network relaxation was also observed. The two components (0.9~4.9 ps and 31~100 ps) of the hydration dynamics reveal relatively fast water motions around the DNA binding pocket, which facilitate the recognition and interaction between the protein and the substrate. The hydration dynamics of protein-DNA complex show that the water motions (2.2~7 ps and 77~156 ps) at the interface, which is still solvent accessible in the presence of DNA as indicated by the steady-state tryptophan emission peaks (337~342 nm), slows down reflecting the rigid water network and tight local structure of the complex, but are still fast enough in the active site and at the entrance of dNTP for the enzyme to incorporate the incoming nucleotide. Similarly, four single-tryptophan-containing mutants of Dpo4 were examined to reveal the water motions around the DNA binding pocket and at the Dpo4 active site. The hydration dynamics indicate that water relaxation is still fast both at the interface (2.3~2.8 ps and 77~84 ps) and in the active site (3 ps and 107 ps), reflecting a flexible structure of water networks in these recognition and binding regions. Further, the hydration dynamics of the active site in the protein-DNA complex show slower water motions (4.8 ps and 164 ps) indicating the rigid water network and local structures after binding of the DNA substrate. Moreover, the anisotropy dynamics reveal that the active site structure of Pol β is rigid, while the active site of Dpo4 is spacious and flexible, which is required to accommodate large DNA lesions in order to perform its translesion replication function.
Dongping Zhong (Committee Chair)
Ralf Bundschuh (Other)
Dehua Pei (Other)
Michael G. Poirier (Other)
206 p.
Biophysics

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Citations

  • Yang, Y. (2009). Ultrafast Hydration Dynamics on Protein Surface and at Protein-DNA Interface [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261450640

    APA Style (7th edition)

  • Yang, Yi. Ultrafast Hydration Dynamics on Protein Surface and at Protein-DNA Interface. 2009. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1261450640.

    MLA Style (8th edition)

  • Yang, Yi. "Ultrafast Hydration Dynamics on Protein Surface and at Protein-DNA Interface." Doctoral dissertation, Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261450640

    Chicago Manual of Style (17th edition)

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This open access ETD is published by The Ohio State University and OhioLINK.