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Heterogeneous solvation shell dynamics around candida antarctica lipase b enzyme using molecular dynamics simulations: relationships with solvent structure, enzyme structure and enzyme dynamics
Dahanayake, Jayangika Niroshani
Dahanayake, Jayangika Niroshani
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Dissertation
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2017-12
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Abstract
Solvent-compatible enzymes (those that function in organic solvents) are an
important field of research. Understanding the relationship between solvent dynamics and
protein dynamics will improve applications of proteins in non-aqueous solvents and
design of solvent systems and engineer proteins for non-aqueous biocatalysis. The main
focus of this dissertation is characterization of local heterogeneous solvation shell
dynamics around Candida Antarctica Lipase B (CALB) enzyme and relating these local
solvation shell dynamics to solvent structure, enzyme structure and enzyme dynamics.
Solvent dynamics were studied under two categories, as hydration layer dynamics and
non-aqueous solvation layer dynamics. Interfacial solvent dynamics at the CALB enzyme
have been characterized by protein-solvent hydrogen bond lifetimes, solvation layer
residence times, reorientation times, and diffusion times of solvation shell solvent
molecules. We have shown that local water dynamics are affected by the protein structure
directly through chemical heterogeneity and topological heterogeneity of protein
structure and indirectly, since the protein structure modulates the local water structure
and these changes in local water structure affect the local water dynamics. Further we
have shown that protein structure influences protein dynamics by modulating the local
solvent structure and providing regions with faster moving water. Validity of Rosenfeld
scaling, which describes the diffusion-entropy relation in liquid water was discovered for
waters in local hydration shell for the first time in this study. As non-aqueous solvents, a
variety of solvents are used in this study; namely, acetonitrile, n-butanol, tert-butanol,
and cyclohexane, and we have shown that that local solvent dynamics have effects on the
local protein flexibilities and these effects depend on the nature of the solvent.
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Thesis (Ph.D.)-- Wichita State University, College of Liberal Arts and Sciences, Dept. of Chemistry
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Wichita State University
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Copyright 2017 by Jayangika N. Dahanayake
All Rights Reserved