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Characterizing Bile Acid Association As a Ligand and In CHARACTERIZING BILE ACID ASSOCIATION AS A LIGAND AND IN MICELLIZATION. By BRIAN SCOTT WERRY Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Adviser: Dr. Gregory P. Tochtrop Department of Chemistry CASE WESTERN RESERVE UNIVERSITY January, 2014 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of Brian S. Werry Candidate for the Doctor of Philosophy degree*. Prof. Blanton S. Tolbert (Chair of the Committee, Department of Chemistry, CWRU) Prof. Gregory P. Tochtrop (Department of Chemistry, CWRU) Prof. Irene Lee (Department of Chemistry, CWRU) Prof. Paul R. Carey (Department of Chemistry, CWRU) Prof. Brian A. Cobb (Department of Pathology, CWRU) Date: November 21st, 2013 * We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Table of Contents ................................................................................................................. i List of Tables ..................................................................................................................... iv List of Figures ......................................................................................................................v Acknowledgements .......................................................................................................... viii List of Abbreviations ......................................................................................................... ix Abstract ............................................................................................................................ xiii Chapter 1. General Introduction ..........................................................................................1 1.1. Bile acids .....................................................................................................................1 1.1.1. Physiologic importance ......................................................................................1 1.1.2. Biosynthesis .......................................................................................................3 1.1.3. Secondary modifications ....................................................................................4 1.1.4. Structural basis as detergents .............................................................................5 1.2. Enterohepatic circulation ............................................................................................7 1.2.1. Molecular biology ..............................................................................................7 1.2.2. Fatty acid binding protein 6 (FABP6) .............................................................10 1.3. Experimental methods ..............................................................................................11 1.3.1. Isothermal titration calorimetry of micellization .............................................11 1.3.2. Isothermal titration calorimetry of protein-ligand binding energetics .............12 1.3.3. Two-dimensional NMR of protein-ligand binding selectivity.........................12 1.4. Scope of the projects .................................................................................................13 1.5. References .................................................................................................................14 Chapter 2. Site-Selective Recognition of Secondary Bile Acid by FABP6 ......................17 i 2.1 Introduction ................................................................................................................17 2.1.1 Secondary bile acid – Lithocholic acid .........................................................17 2.1.2 FABP6...........................................................................................................17 2.2. Results and Discussion .............................................................................................19 2.3. Materials and Methods ..............................................................................................36 2.4 References ..................................................................................................................40 Chapter 3. Statistical Determination of a Bile Acid Micellization Model .........................43 3.1. Introduction ...............................................................................................................43 3.1.1. Bile acid self-association: Small’s model ....................................................43 3.1.2. Micelle polydispersity ..................................................................................47 3.1.3. Isothermal titration calorimetry of demicellization .....................................48 3.2. Proposed study ..........................................................................................................49 3.3. Results and Discussion .............................................................................................50 3.3.1. Uniform micellar system model...................................................................52 3.3.2. Non-uniform sequential stepwise model .....................................................57 3.3.3. Non-uniform multimer model ......................................................................61 3.4 Conclusion .................................................................................................................67 3.5 Materials and Methods ...............................................................................................69 3.6 References ..................................................................................................................71 Chapter 4. Evolutionary Significance of C24 Bile Acids’ Micellization Characteristics ..75 4.1. Introduction ...............................................................................................................75 4.1.1. Bile acids as physiological detergents .........................................................75 4.1.2. Diversity of bile acid chemical structure .....................................................76 ii 4.1.3. Bile acid side chain modification .................................................................78 4.1.4. Purposed study .............................................................................................79 4.2. Results and Discussion .............................................................................................80 4.3. Materials and Methods ..............................................................................................90 4.3.1. Synthetic procedures ....................................................................................91 4.4 References ..................................................................................................................98 Appendix I. Origin C fitting functions ...............................................................................99 Appendix II. NMR spectra of synthesized compounds ...................................................103 Bibliography ....................................................................................................................129 iii List of Tables Table 1.1.1. Nomenclature and relative abundance in human bile ....................................2 Table 1.1.2. Critical micellar concentrations for physiologically abundant bile acids ......7 Table 2.2.1. Stepwise binding parameters for 1:9 bile acid mixtures with hFABP6 .......24 Table 3.3.1. Parameter values from the uniform model fitting to ITC experimental data of the demicellization of CA, CDCA, and DCA ...............................................................56 Table 3.3.2. Parameter values from the non-uniform sequential stepwise model fitting to ITC experimental data of the demicellization of CA, CDCA, and DCA ..........................60 Table 3.3.3. Parameter values from the non-uniform bi-micelle multimer model fitting to ITC experimental data of the demicellization of CA, CDCA, and DCA ..........................64 Table 3.3.4. Parameter values from the non-uniform tri-micelle multimer model fitting to ITC experimental data of the demicellization of CA, CDCA, and DCA ......................66 Table 4.2.1. Thermodynamic parameters for the micellization of CA and CDCA side chain derivatives calculated from the bi-micelle multimer model .....................................83 Table 4.2.2. Interpolated thermodynamic parameters for micellization of CA and CDCA side chain derivatives at 37°C ............................................................................................84 iv List of Figures Figure 1.1.1. Chemical structure of cholesterol and various bile acids .............................2 Figure 1.1.2. Schematic representation of bile acid synthesis............................................... 4 Figure 1.1.3. Structural diversity of primary and secondary bile acids .............................5 Figure 1.1.4. Ring conformation of cholic acid .................................................................6 Figure 1.2.1. Molecular biology of the enterohepatic circulation ......................................9 Figure 2.2.1. Calorimetric results for LCA binding to human FABP6 ............................21 Figure 2.2.2. Calorimetric results for LCA and CA binding to human FABP6 ..............22 Figure 2.2.3. Calorimetric results for 1:9 ratio mixtures of LCA:CA and CDCA:CA binding to
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