Thesis (Ph. D.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 82-86). Also available on the World Wide Web.

Thesis (Ph. D.)--University of New South Wales, 2003. / Also available online.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004. / Includes bibliographical references (leaves 103-113). Also available in electronic version. Access restricted to campus users.

Thesis (Ph. D.)--Lehigh University, 2006. / Includes vita. Includes bibliographical references (leaves 117-125).

The goals of this project were to synthesize voltage-gated ion channels based upon previously studied pore-formers and to further explore the mechanism of ion transport with this type of pore-former. The syntheses of bis-macrocyclic bola-amphiphiles started with two different macrocycles prepared via a two-step cyclization from maleic anhydride by reaction with 1,8-octanediol alone or with triethyleneglycol. The macrocycles were then modified to a set of mono-adducts and bis-adducts by Michael addition of thiols (3-mercaptopropanol, 2-mercaptoacetic acid, or 3-mercaptopropionic acid). The mercaptopropanol adduct was converted to a mesylate and coupled with a carboxylate derivative to form a bis-macrocycle. Repetitious gel permeation chromatography gave a bis-macrocycle bearing only one head group, a carboxylate. The second head group was added via Michael addition to give a bis-macrocyclic bola-amphiphile which could have either the same head groups or different head groups. Two symmetrical transporters were synthesized via another route: two macrocycles reacted with 2-mercaptoethyl sulfide to generate a bis-macrocycle, and the same head group was then simultaneously added to both ends to give a symmetrical bola-amphiphile. Transporters with different combinations of head groups were synthesized to compare head group effects on cation transport properties, while different macrocycles were used in the backbone of transporter candidates to give two series of compounds for comparison of their behaviors. The second phase of this project investigated the transport properties of candidates using pH-stat titration. The pH-stat titration of bilayer vesicles allowed determination of dynamic transport properties: transport rate, apparent kinetic order and cation selectivity. Combined with information from planar bilayer experiments (done by D. Loock), it was found that an asymmetrical bis-macrocyclic bola-amphiphile with an acetate and a succinate head group behaves as voltage-gated ion channel in planar bilayers. An ion transport mechanism of the present system was proposed which involves the formation of active aggregates (probably dimers or oligomers). / Graduate

No description available.

Acid-sensing ion channels (ASICs) are trimeric, sodium-selective proton-gated ion channels. Having ligands as small as protons presents a challenge when studying the structure-function relationships of pH-dependent gating. Knowing where protons must bind to evoke a pH-dependent conformational change related to gating would provide one with insights into the molecular mechanisms underlying pH-dependent function in ASICs. We use molecular dynamics (MD) simulations that allow us to model explicit protons and directly examine the effects of changing protonation states on ASIC1 dynamics. We first combine the use of unbiased MD simulations with pKₐ prediction on the three functional states of cASIC1 to identify the effects of protonation state changes on interactions between ionizable residues in the acidic pocket (ACP), a region rich in acidic residues in the protein that plays a role in pH-sensing. We interpret the importance of E98, a buried residue in the ACP with a highly shifted pKₐ value, as well as the positively charged R191, also in the ACP, which has a flexible side chain and can interact with multiple negatively charged side chains, and the role of these residues in the pH-dependent collapse of the ACP. Additionally, we identify a hydrogen-bond network in the palm domain that consists of the Q277 side chain that interacts with the E80 side chain and L414 backbone carbonyl. This network contributes to a stable desensitized state and is stabilized by an E80-/E412H/E417H protonation configuration. Next, targeted MD was combined with pKₐ prediction to simulate the full transition pathways and to link protonation states with the molecular mechanisms involved in conformational changes. Our results suggest four residues, E98, E314, H328, and E374, that may be important in pH-sensing and gating, and that require further functional investigation in the context of activation and desensitization. This research exemplifies how MD is a useful tool in studying how protonation directly affects the structural dynamics of a protein and how it can complement existing functional studies and be used to suggest future experimental investigations.

Graduate

No description available.

Excitable cells display dynamically regulated changes in the properties of ion currents during development. These changes are crucial for the proper maturation of cellular excitability, and therefore have the potential to affect more sophisticated functions, including neural circuits, movements, and behaviors. Zebrafish skeletal muscle is an excellent model for studying the development of ion channels and their contributions to excitability. They possess distinguishable populations of red and white muscle fibers, whose biological functions are well understood. The main objectives of this thesis were: (1) To characterize the development of muscle excitability by examining properties of voltage-gated sodium and potassium currents expressed in embryonic and larval zebrafish during the first week of development. (2) To elucidate some of the mechanisms by which ion current development might be controlled, beginning with activity-dependent and phosphorylation-dependent mechanisms. These objectives were approached using whole-cell electrophysiological techniques to examine the voltage-dependent and kinetic properties of voltage-gated sodium and potassium currents in intact zebrafish skeletal muscle preparations. Mutant sofa potato zebrafish, which lack functional nicotinic acetylcholine receptors, were then utilized to determine whether synaptic activity at the neuromuscular junction is required for proper ion current development. Finally, protein kinases were activated pharmacologically in order to determine whether they were able to modulate ion currents during development. The results revealed that properties of ion currents undergo a developmental progression, including increased current density, accelerated kinetics, and shifts in voltage-dependence; these developments correlated well with the maturation of muscle action potentials and the movements and behaviors they mediate. Sofa potato mutants were found to be deficient in certain aspects of ion current development, but other aspects appeared to be unaffected by a lack of synaptic activity. Protein kinase A demonstrated the ability to drastically reduce potassium current density; however the effects of PKA were similar at all developmental stages. Overall, these findings provide novel insight into the roles played by voltage-gated currents during the development of excitability in zebrafish skeletal muscle, and expand the rapidly growing body of knowledge about ion channel function in general. / Physiology, Cell & Developmental Biology