This dissertation reports on the recent discovery that calix[4]pyrrole not only functions as an anion receptor, but also has the ability to act as an ion pair receptor. It was discovered that in the solid state large diffuse cations, such as Cs+ and imidazolium, will occupy the electron-rich cone-like cavity that is formed upon anion binding to the NH region of the calix[4]pyrrole core. Also discussed are efforts devoted to improving the anion binding ability of calixpyrroles and fine-tuning their inherent selectivity. This has been probed through a variety of structural modifications. One of the most attractive of the modification strategies currently being explored involves expansion of the central binding cavity by using higher order β-fluorinated calix[n]pyrroles; n = 5, 6, and 8. An advantage of β-fluorinated calix[4]pyrrole is that it shows enhanced anion binding affinities toward several anions compared to the parent calix[4]pyrrole. Fluorinated calixpyrroles have also shown an ability to extract anions from aqueous environments into organic media. An alternative strategy has been to attach “straps” resulting in bicyclic systems, which further define the binding cavity achieving higher affinity and anion selectivity. The binding interactions of calixpyrrole and it derivative have been quantified using analytical techniques, such as nuclear magnetic resonance spectroscopy and isothermal titration calorimetry. The results of these latter studies will be discussed herein. / text

This diploma thesis dealt with the study of interactions of soil organic matter, specifically humic acids with a pollutant, where the surfactant Septonex was used. Humic acids were isolated from two different soils in the work, namely black earth and cambium. The theoretical part describes the formation of humic acids as such, their possible interactions with substances and the characterization of surfactants. The experimental part is devoted to the characteristics of humic acids using elemental analysis, thermogravimetry and then the most important part of the thesis, namely the monitoring of interactions using isothermal titration calorimetry. The experiment showed that the sample of isolated black earth at the surfactant concentration of 0,075 molâdm3 had the best interaction with the surfactant.

Copper is an essential element for all living organisms. However, due to its low redox potential it can be involved in the production of reactive oxygen species; where excess amounts of copper can be exceptionally toxic.1 In humans, malfunctions in copper metabolism are linked to diseases such as Menkes syndrome, Wilson’s disease, prion disease, and Alzheimer’s disease.2 Maintenance of copper homeostasis requires a number of proteins, such as copper transporters and chaperones to deliver copper to the correct protein while limiting free copper in the cell.3 Therefore, understanding the thermodynamics of copper(II) coordination in proteins is critical to our understanding of copper homeostasis. Herein we report human carbonic anhydrase II contains a novel copper binding site with picomolar affinity.4 A full characterization of the structure and thermodynamics associated with the coordination of both Cu atoms into their respective sites is discussed. Techniques including paramagnetic nuclear magnetic resonance spectroscopy (NMR), and x-ray absorption spectroscopy (XAS) techniques provide insight into the high affinity CuA coordination environment. A detailed characterization of this high affinity binding site and related peptide-bound model complexes are included, with the results providing insights into the chemistry and physiological impact of copper binding in human carbonic anhydrase II.

Carbonic anhydrase (CA) is a well-studied, zinc dependent metalloenzyme that catalyzes hydrolysis of carbon dioxide to the bicarbonate ion. In the past, metal binding studies related to CA have continually relied on equilibrium dialysis measurements to ascertain an extremely strong association constant (Ka= approx. 1.2 x 1012) for Zn2+. However, new methodology has allowed us to collect data using isothermal titration calorimetry (ITC), which calls that number and the association constants for many other first row transition metal ions into question. Thermodynamic parameters associated with Zn2+, Cu2+, Ni2+, and Co2+ binding to apoCA are unraveled from a series of complex equilibria associated with the in vitro metal binding event. This in-depth analysis adds clarity to the complex ion chemistry associated with metal ion binding to carbonic anhydrase and validates thermochemical methods that accurately measure association constants and thermodynamic parameters for complex-ion and coordination chemistry observed in vitro. Additionally, the as-isolated and the reconstituted ZnCA and other metalsubstituted CAs were probed using X-ray absorption spectroscopy. Both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses indicate the metal centers in the reconstituted carbonic anhydrases offer new metal binding coordination sites that can be used as models to understand nonheme metal sites in vivo.

A series of phosphotripeptide ligands for the Grb2 SH2 domain was designed and synthesized, each of which derived from the minimal consensus sequence required for binding: Ac-pYXN. The binding affinity and related thermodynamic parameters were determined by isothermal titration calorimetry. Both the size and connectivity of the side-chain was varied. The consequences of incorporating α,α-disubstitution at the pY+1 residue on binding thermodynamics were evaluated, as were the effects of constraining the side-chains in a ring. The series was evaluated from a number of perspectives: (1) increasing size of the pY+1 residue by utilizing various amino acid types: monoalkyl, dialkyl, or cycloalkyl; (2) comparisons between ligands with the same number of carbons (scission control); and (3) by comparing ligands incorporating cyclic pY+1 residues with those incorporating α,α-dialkyl residues with one fewer methylene group (excision control). Inconsistencies in the thermodynamic consequence of constraining the backbone were observed within this set of ligands, which reveal the limitations of our understanding of protein-ligand interactions. Aspects of both the classical and non-classical hydrophobic effect were observed, but the occurance of one over the other could not be explained. / text

Pterin-4a-carbinolamine dehydratase (PCD) is an essential component of the phenylalanine hydroxylase (PAH) system, catalyzing the regeneration of the essential cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin [6(R)BH4]. Mutations in PCD or its deactivation by hydrogen peroxide result in the generation of 7(R,S)BH4, which is a potent inhibitor of PAH that has been implicated in primapterinuria, a variant form of phenylketonuria, and in the skin depigmentation disorder vitiligo. We have synthesized and separated the 7(R) and 7(S) diastereomers confirming their structure by NMR. Both 7(R)- and 7(S)BH4 function as poor cofactors for PAH, whereas only 7(S)BH4 acts as a potent competitive inhibitor vs. 6(R)BH4 (Ki=2.3-4.9 µM). Kinetic and binding studies, as well as characterization of the pterin-enzyme complexes by fluorescence spectroscopy, revealed that the inhibitory effects of 7(R,S)BH4 on PAH are in fact specifically based on 7(S)BH4 binding. The molecular dynamics simulated structures of the pterin-PAH complexes indicate that 7(S)BH4 inhibition is due to its interaction with the polar region at the pterin binding site close to Ser-251, whereas its low efficiency as cofactor is related to a suboptimal positioning toward the catalytic iron. 7(S)BH4 is not an inhibitor for tyrosine hydroxylase (TH) in the physiological range, presumably due to the replacement of Ser-251 by the corresponding Ala297. Taken together, our results identified structural determinants for the specific regulation of PAH and TH by 7(S)BH4, which in turn aid in the understanding of primapterinuria and acute vitiligo. Pey, A. L., Martinez, A., Charubala, R., Maitland, D. J., Teigen, K., Calvo, A., Pfleiderer, W., Wood, J. M., Schallreuter, K. U. Specific interaction of the diastereomers 7(R)- and 7(S)-tetrahydrobiopterin with phenylalanine hydroxylase: implications for understanding primapterinuria and vitiligo Pterin-4a-carbinolamine dehydratase (PCD) is an essential component of the phenylalanine hydroxylase (PAH) system, catalyzing the regeneration of the essential cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin [6(R)BH4]. Mutations in PCD or its deactivation by hydrogen peroxide result in the generation of 7(R,S)BH4, which is a potent inhibitor of PAH that has been implicated in primapterinuria, a variant form of phenylketonuria, and in the skin depigmentation disorder vitiligo. We have synthesized and separated the 7(R) and 7(S) diastereomers confirming their structure by NMR. Both 7(R)- and 7(S)BH4 function as poor cofactors for PAH, whereas only 7(S)BH4 acts as a potent competitive inhibitor vs. 6(R)BH4 (Ki=2.3-4.9 µM). Kinetic and binding studies, as well as characterization of the pterin-enzyme complexes by fluorescence spectroscopy, revealed that the inhibitory effects of 7(R,S)BH4 on PAH are in fact specifically based on 7(S)BH4 binding. The molecular dynamics simulated structures of the pterin-PAH complexes indicate that 7(S)BH4 inhibition is due to its interaction with the polar region at the pterin binding site close to Ser-251, whereas its low efficiency as cofactor is related to a suboptimal positioning toward the catalytic iron. 7(S)BH4 is not an inhibitor for tyrosine hydroxylase (TH) in the physiological range, presumably due to the replacement of Ser-251 by the corresponding Ala297. Taken together, our results identified structural determinants for the specific regulation of PAH and TH by 7(S)BH4, which in turn aid in the understanding of primapterinuria and acute vitiligo. / ¿ ¿

In this thesis, on the basis of the asymmetrical charge distribution of E. coli topoisomerase I, I developed a new rapid procedure to purify E. coli DNA topoismoerase I in the milligram range. The new procedure includes using both cation- and anion-exchange columns, i.e., SP-sepharose FF and Q-sepharose FF columns. E. coli topoisomerase I purified here is free of nuclease contamination. The kinetic constants of the DNA relaxation reaction of E. coli DNA topoisomerase I were determined as well. I also used isothermal titration calorimetry to investigate the energetics of DNA supercoiling by using the unwinding properties of DNA intercalators, ethidium and daunomycin. After comparing the enthalpy changes of these DNA intercalators binding to supercoiled and nicked or relaxed plasmid DNA pXXZ06, I determined the DNA supercoiling enthalpy is about 12 kcal/mol per turn of DNA supercoil, which is in good agreement with the previously published results.

The 2-His-1-carboxylate facial triad is a common metal binding motif among nonheme iron(II) enzymes. Made up of two histidine side chain residues, and one carboxylate side chain of either a glutamate or aspartate residue occupying one face of the iron(II) octahedral coordinating sphere, the 2-His-1-carboxylate motif provides proximity of substrate(s) and molecular oxygen for important oxidation reactions in biological chemistry. Computational, structural, and kinetic analyses have afforded mechanistic details on how these enzymes control the oxidation reactions they catalyze; from the oxidation state of the metal center to the supporting interactions from secondary sphere amino acid residues. However, the extensive literature on the 2-His-1-carboxylate facial triad enzymes currently contains deficiencies in the area of fundamental, experimental thermodynamic analyses of metal and substrate binding in these systems. The focus of this study is to determine the energetics of substrate and metal binding to two representative enzymes of the 2-His-1-carboxylate facial triad-containing family. More specifically, we examine iron(II) binding to the alpha-ketoglutarate- dependent model system alpha-ketoglutarate/taurine dioxygenase, and substrate binding to a well-known extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase. Using isothermal titration calorimetry, we are able to determine equilibrium constants, enthalpies, entropies and Gibbs free energies for the binding reactions, affording new insight into what drives the reactions forward at the 2-His-1-carboxylate facial triad active site center.

Rare Earth Elements (REEs: La–Lu, Y, and Sc) are critical components for technological innovations, therefore more effective methods for the domestic extraction and purification of REEs are in ever-increasing demand. Metal-chelating polymers have great potential in these applications due to their relatively low cost and high affinity for target elements. However, while much research has focused on specific ligands attached to polymers, little is known about the effect of polymer architecture itself on metal chelation. This dissertation reports recent progress in the design, synthesis, and application of polymers for the chelation of various REEs. In addition to synthesizing a series of metal-chelating polymers, we elucidated the thermodynamics of binding using isothermal titration calorimetry (ITC) to gain insight into the specific relationship between polymer structure and metal binding. ITC enables the direct measurement of the binding affinity (Ka), enthalpy changes (ΔH), and stoichiometry of the interactions between macromolecules and metal ions in solution. The thermodynamics of metal chelation underpins many technologies for REE extraction. Consequently, elucidating these parameters enables the rational design of future materials. / Doctor of Philosophy / Rare-Earth Elements (REEs) are critical metals used in many modern technologies, therefore more effective methods for the recovery and purification of REEs are in ever-increasing demand. Metal-chelating polymers—materials that can bind metals—have great potential in these applications due to their relatively low cost and high affinity for target elements. However, while much research has focused on the specific metal-binding group attached to the polymer, little is known about the effect of polymer architecture itself on metal chelation. This dissertation reports recent progress in the design, synthesis, and application of materials that bind to various REEs. In addition to synthesizing a series of metal-binding polymers, we measured the heat absorbed or produced during metal-binding interactions. These experiments produced fundamental insights into the interactions between the polymers, metals ions, and water molecules in solution. Overall, this work produces a depiction of the polymer–metal binding process, which enables insight into each polymer's properties as a metal-binding material. Future researchers can use these guidelines to develop the next generation of materials for the extraction of these critical metals.

No / Pterin-4a-carbinolamine dehydratase (PCD) is an essential component of the phenylalanine hydroxylase (PAH) system, catalyzing the regeneration of the essential cofactor 6(R)-L-erythro-5,6,7,8-tetrahydrobiopterin [6(R)BH4]. Mutations in PCD or its deactivation by hydrogen peroxide result in the generation of 7(R,S)BH4, which is a potent inhibitor of PAH that has been implicated in primapterinuria, a variant form of phenylketonuria, and in the skin depigmentation disorder vitiligo. We have synthesized and separated the 7(R) and 7(S) diastereomers confirming their structure by NMR. Both 7(R)- and 7(S)BH4 function as poor cofactors for PAH, whereas only 7(S)BH4 acts as a potent competitive inhibitor vs. 6(R)BH4 (Ki=2.3–4.9 μM). Kinetic and binding studies, as well as characterization of the pterin-enzyme complexes by fluorescence spectroscopy, revealed that the inhibitory effects of 7(R,S)BH4 on PAH are in fact specifically based on 7(S)BH4 binding. The molecular dynamics simulated structures of the pterin-PAH complexes indicate that 7(S)BH4 inhibition is due to its interaction with the polar region at the pterin binding site close to Ser-251, whereas its low efficiency as cofactor is related to a suboptimal positioning toward the catalytic iron. 7(S)BH4 is not an inhibitor for tyrosine hydroxylase (TH) in the physiological range, presumably due to the replacement of Ser-251 by the corresponding Ala297. Taken together, our results identified structural determinants for the specific regulation of PAH and TH by 7(S)BH4, which in turn aid in the understanding of primapterinuria and acute vitiligo. —Pey, A. L., Martinez, A., Charubala, R., Maitland, D. J., Teigen, K., Calvo, A., Pfleiderer, W., Wood, J. M., Schallreuter, K. U. Specific interaction of the diastereomers 7(R)- and 7(S)-tetrahydrobiopterin with phenylalanine hydroxylase: implications for understanding primapterinuria and vitiligo