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Life Sciences Commons

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2004

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Biochemistry, Biophysics, and Structural Biology

University of Iowa

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Full-Text Articles in Life Sciences

Energetics Of Ion-Protein Interactions, Travis Tyson Waldron Jan 2004

Energetics Of Ion-Protein Interactions, Travis Tyson Waldron

Theses and Dissertations

In keeping with the goals of our laboratory, efforts in this thesis are directed towards improving our understanding, and therefore our ability to calculate, the energetics of protein-ligand interactions. Electrostatic contributions to protein-ligand binding events are poorly understood, and underrepresented in data sets used to parameterize the energetics of protein unfolding and binding. Therefore, the focus in this thesis is placed on ion-protein interactions as model systems that can give insight into the contribution of charge-charge interactions to the enthalpy, entropy, and heat capacity changes associated with binding. In order to measure the energetics of charge-charge interactions, both differential scanning ...


Energetic Consequences Of Structural Features And Dynamics Changes Upon Nucleotide Binding To Ribonuclease Sa: Molecular Basis For Nucleotide Binding Specificity, Greta Lynn Schrift Jan 2004

Energetic Consequences Of Structural Features And Dynamics Changes Upon Nucleotide Binding To Ribonuclease Sa: Molecular Basis For Nucleotide Binding Specificity, Greta Lynn Schrift

Theses and Dissertations

Proteins are often able to distinguish between closely related ligands, thus achieving specificity. A major goal in biophysical chemistry is to understand the molecular basis for protein-ligand recognition. This level of understanding is necessary for developing methods to accurately predict protein-ligand binding energetics from structural data. The goal of this thesis was to identify features of protein-ligand interactions that may not be adequately accounted for in structure energetics calculations in order to improve our ability to predict binding energetics for these interactions. Specifically, the features of protein-nucleotide binding were studied using the small, guanine-specific ribonuclease, RNase Sa binding to two ...