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Ultrafast Collective Dynamics of Water-Protein Interactions

Houston, Patrick R.
http://orcid.org/0000-0001-5587-3480
http://rave.ohiolink.edu/etdc/view?acc_num=osu1598458748735467

Abstract Details

2020, Doctor of Philosophy, Ohio State University, Biophysics.
All life on earth is bathed in water. Protein, the fundamental machinery of life, requires water to maintain structural stability and function. Thus, in order to understand the structure, dynamics, and therefore function, of proteins, one must also understand the fundamental physical and dynamic properties of the water that surrounds them, as well as the interactions between water and protein. This dissertation investigates the ultrafast dynamics occurring in the hydration shell, extending out 10 Å from the protein surface. Using tryptophan as an intrinsic optical probe with ultrafast fluorescence upconversion spectroscopy, we probe the dynamics of water within the hydration shell as well as local protein motions, with single site specificity and femtosecond temporal resolution. In this work, we will first use this methodology to probe the hydration shell dynamics of a tightly packing protein, then investigate the nature of protein-water coupling by investigating the energetic landscape behind hydration shell dynamics. First, we investigated hydration shell of the fish eye lens protein γM7-crystallin which is found in extremely high concentrations in vivo, nearing the packing limit. Through our methodology combined with NMR nuclear spin relaxation, we observed correlated fluctuations of the hydration shell and protein sidechain on the timescales of picoseconds and hundreds of picoseconds, corresponding to local reorientations and hydration network reorientations. Interestingly, we observed slowed motions on the hundreds of picoseconds timescale when compared to proteins of similar secondary structure, which we conclude may influence the enhanced packing ability of this protein. Next we characterized the nature of protein-water coupling within the hydration shell. First, we investigated the hydration belt around a globular, β-barrel protein, rat liver fatty acid-binding protein (rLFABP). We measured water and protein fluctuations over a range of temperatures from 2 °C to 40 °C. We observed coupled water and protein dynamics on timescales of tens and hundreds of picoseconds over the entire hydration belt. Interestingly, we found that the water and protein dynamics are linearly correlated with temperature through the origin, with water dynamics always occurring faster than protein dynamics. We also uncovered the activation energy barrier governing solvent and protein fluctuations and found that these barriers are uniform over the entire protein. Significantly, the barriers are higher than other proteins we have studied previously suggesting a rigid water network over the surface of the protein. Finally, we conducted temperature-dependent solvation studies on the B1 subunit of protein G (GB1), a small, 56 amino-acid protein. Like rLFABP, we observed a temperature correlated water and protein dynamics over the surface of the protein and a common activation energy barrier for all exposed mutants. However, GB1 is characterized by a novel solvation process, occurring at many hundreds of picoseconds. We find that this motion is linearly correlated with temperature to the slow motion on tens of picoseconds, found in all protein systems, and has the same energy barrier as this motion. Thus, we found that these novel dynamics indicate coupled a slow water network fluctuation coupled to large-amplitude protein motions possibly encompassing correlated backbone motions.
Dongping Zhong, Ph.D. (Advisor)
Marcos Sotomayor, Ph.D. (Committee Member)
Sherwin Singer, Ph.D. (Committee Member)
Zhengrong Wu, Ph.D. (Committee Member)
133 p.
Biochemistry; Biophysics; Physical Chemistry; Physics
hydration shell dynamics; protein sidechain fluctuations; coupled motions; tryptophan scan; femtosecond fluorescence spectroscopy

Recommended Citations

Citations

  • Houston, P. R. (2020). Ultrafast Collective Dynamics of Water-Protein Interactions [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1598458748735467

    APA Style (7th edition)

  • Houston, Patrick. Ultrafast Collective Dynamics of Water-Protein Interactions. 2020. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1598458748735467.

    MLA Style (8th edition)

  • Houston, Patrick. "Ultrafast Collective Dynamics of Water-Protein Interactions." Doctoral dissertation, Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1598458748735467

    Chicago Manual of Style (17th edition)

osu1598458748735467
32
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This open access ETD is published by The Ohio State University and OhioLINK.