Date of Award

Fall 12-2014

Degree Type


Degree Name


Degree Program




Major Professor

Steven Rick

Second Advisor

Mark Trudell

Third Advisor

Richard Cole

Fourth Advisor

David Mobley


Various studies suggest tannins act as antioxidants, anticarcinogens, cardio-protectants, anti-inflammatory agents, and antimicrobials. However, more investigation is needed to examine the bioavailability of tannins. Tannins bind to salivary peptides by hydrophilic and hydrophobic mechanisms. Electrospray Ionization Mass Spectrometry (ESI-MS) has been used to assess both hydrophilic and hydrophobic components of protein complexes. ESI-MS could potentially be an effective tool for screening the bioavailability of tannins. Weaker binding tannins are predicted to be more highly absorbed by the body, and should therefore exhibit greater bioavailability. Rannulu and Cole have used ESI-MS to measure binding affinities of procyanidin tannin stereoisomers for salivary peptides in aqueous solution. The condensed tannins procyanidin B1, B2, B3, and B4 demonstrated significantly different binding affinities (binding strengths) for the Histatin 5 salivary peptide. The procyanidin-Histatin 5 binding mechanisms in the ESI-MS experiments by Rannulu and Cole were investigated using the FRED docking program combined with molecular dynamics optimization in the AMBER software suite. The simulations suggest residual liquid-phase binding interactions in procyanidin-Histatin 5 complexes are maintained in the gas phase under conditions resembling those in ESI-MS experiments, though the gas-phase interaction energies were enhanced. Increased hydrogen bonding and decreased π-π stacking interactions were also detected in gas versus liquid-phase procyanidin-Histatin 5 complexes. In addition, simulation results suggest multiple conformations of procyanidins bind Histatin 5 at several sites and procyanidin binding does not fix the Histatin 5 peptide backbone. The simulations agree with previous studies which indicate aromatic Histatin 5 residues are responsible for procyanidin-Histatin 5 binding and tannins can bind salivary peptides in multiple conformations.

The effects of Hofmeister salts on complexation of an amphiphilic guest adamantane carboxylic acid to the hydrophobic surface of a deep-cavity cavitand have been investigated by Gibb et al. Adamantane-cavitand binding was found to be largely enthalpically driven, though adamantane binding in the presence of the salting-in anions perchlorate and thiocyanate was entropically driven. Gibb et al. also found that perchlorate-cavitand binding was enthalpically favorable, though entropically unfavorable. Potential-of-mean-force (PMF) calculations for perchlorate-cavitand and thiocyanate-cavitand complexation were performed using umbrella sampling with a modified version of the sander module from the Amber 9 software suite to further investigate the thermodynamic properties of Hofmeister-anion binding to the hydrophobic cavitand. The enthalpy for salting-in anion-cavitand complexation was calculated from the potential energy difference between the bound and unbound state (the potential energy of binding) along with the entropy. The binding entropy and enthalpy were also calculated using a finite difference approximation to the entropy. The enthalpy for perchlorate-cavitand complexation calculated from the binding energy and the finite difference approximation to the entropy was favorable with an unfavorable entropy. The binding enthalpy and entropy for thiocyanate-cavitand complexation calculated from the binding energy and finite difference approximation to the entropy were unfavorable and favorable, respectively, perhaps due to a classical hydrophobic effect. The orientation of the ligand, the number of water molecules displaced from the ligand and cavitand upon complexation, and the number of nearest-neighbor atom contacts between the ligand and the cavitand were also calculated. Additionally, the energetics of various interactions involved in salting-in anion-cavitand complexation including the anion-cavitand, anion-water, cavitand-water, and water-water interactions were assessed, though the data were inconclusive.


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