The nervous system, including the brain, is a complex network with billions of complex neurons. Ion channels mediate the electrical signals that neurons use to integrate input and produce appropriate output, and could thus be thought of as key instruments in the neuronal orchestra. In the field of neuroscience we are not only curious about how our brains work, but also strive to characterize and develop treatments for neural disorders, in which the neuronal harmony is distorted. By modulating ion channel activity (pharmacologically or otherwise) it might be possible to effectively restore neuronal harmony in patients with various types of neural (including channelopathic) disorders. However, this exciting strategy is impeded by the gaps in our understanding of ion channels and neurons, so more research is required. Thus, the aim of this thesis is to improve the understanding of how specific ion channel types contribute to shaping neuronal dynamics, and in particular, neuronal integration, excitability and memory. For this purpose I have used computational modeling, an approach which has recently emerged as an excellent tool for understanding dynamically complex neurophysiological phenomena. In the first of two projects leading to this thesis, I studied how neurons in the brain, and in particular their dendritic structures, are able to integrate synaptic inputs arriving at low frequencies, in a behaviorally relevant range of ~8 Hz. Based on recent experimental data on synaptic transient receptor potential channels (TRPC), metabotropic glutamate receptor (mGluR) dynamics and glutamate decay times, I developed a novel model of the ion channel current ITRPC, the importance of which is clear but largely neglected due to an insufficient understanding of its activation mechanisms. We found that ITRPC, which is activated both synaptically (via mGluR) and intrinsically (via Ca2+) and has a long decay time constant (τdecay), is better suited than the classical rapidly decaying currents (IAMPA and INMDA) in supporting low-frequency temporal summation. It was further concluded that τdecay varies with stimulus duration and frequency, is linearly dependent on the maximal glutamate concentration, and might require a pair-pulse protocol to be properly assessed. In a follow-up study I investigated small-amplitude (a few mV) long-lasting (a few seconds) depolarizations in pyramidal neurons of the hippocampal cortex, a brain region important for memory and spatial navigation. In addition to confirming a previous hypothesis that these depolarizations involve an interplay of ITRPC and voltage-gated calcium channels, I showed that they are generated in distal dendrites, are intrinsically stable to weak excitatory and inhibitory synaptic input, and require spatial and temporal summation to occur. I further concluded that the existence of multiple stable states cannot be ruled out, and that, in spite of their small somatic amplitudes, these depolarizations may strongly modulate the probability of action potential generation. In the second project I studied the axonal mechanisms of unmyelinated peripheral (cutaneous) pain-sensing neurons (referred to as C-fiber nociceptors), which are involved in chronic pain. To my knowledge, the C-fiber model we developed for this purpose is unique in at least three ways, since it is multicompartmental, tuned from human microneurography (in vivo) data, and since it includes several biologically realistic ion channels, Na+/K+ concentration dynamics, a Na-K-pump, morphology and temperature dependence. Based on simulations aimed at elucidating the mechanisms underlying two clinically relevant phenomena, activity-dependent slowing (ADS) and recovery cycles (RC), we found an unexpected support for the involvement of intracellular Na+ in ADS and extracellular K+ in RC. We also found that the two major Na+ channels (NaV1.7 and NaV1.8) have opposite effects on RC. Furthermore, I showed that the differences between mechano-sensitive and mechano-insensitive C-fiber types might reside in differing ion channel densities. To conclude, the work of this thesis provides key insights into neuronal mechanisms with relevance for memory, pain and neural disorders, and at the same time demonstrates the advantage of using computational modeling as a tool for understanding and discovering fundamental properties of central and peripheral neurons. / <p>QC 20120914</p>

<p>Physical forces play a key role in the morphogenesis of embryos. As cells and tissues change shape, grow, and migrate, they exert and respond to forces via mechanosensitive proteins and protein complexes. How the response to force is regulated is not completely understood. </p><p>Dorsal closure in Drosophila is a model system for studying cell sheet forces during morphogenesis. We demonstrate a role for mechanically gated ion channels (MGCs) in dorsal closure. Microinjection of GsMTx4 or GdCl₃, inhibitors of MGCs, blocks closure in a dose-dependent manner. UV-mediated uncaging of intracellular Ca<super>2+</super> causes cell contraction whereas the reduction of extra- and intracellular Ca<super>2+</super> slows closure. Pharmacologically blocking MGCs leads to defects in force generation via failure of actomyosin structures during closure, and impairs the ability of tissues to regulate forces in response to laser microsurgery.</p><p>We identify three genes which encode candidate MGC subunits that play a role in dorsal closure, <italic>ripped pocket</italic>, <italic>dtrpA1</italic>, and <italic>nompC</italic>. We find that knockdown of these channels either singly or in combination leads to defects in force generation and cell shapes during closure. </p><p>Our results reveal a key role for MGCs in closure, and suggest a mechanism for the coordination of force producing cell behaviors across the embryo.</p> / Dissertation

The self-assembled complex (Pden)4(bipy)4+8 is potentially suited as a portal for synthetic ion channels (Pden = (1, 2-ethylenediamine) Pd(II), bipy = 4, 4'-bipyridine). This thesis examines the solution speciation of mixtures of Pden and bipy and the ion channel activity of the proposed channel. A model which describes the concentration of the species in solution as a function of pH and Pden:bipy ratio was developed. The method determines the solution speciation by solving the mass balance equation for each species using the total concentration of Pden, bipy and H+ and the cumulative formations constants for species in solution. This model is general and can be applied to other systems provided that the cumulative macroscopic formation constants (logßpbh) of the species are either known or can be estimated. The cumulative macroscopic formation constant for a species is determined by an additive free energy process as the sum of the logarithms of a microscopic formation constant (logß'pbh) and a statistical factor (logY). Values for logß'pbh were estimated using stepwise formation constants (logK) for model systems which were determined by potentiometric titration. Values for logY were calculated from the symmetries of the species. The model calculates the concentration of each species as a function of pH and Pden:bipy ratio to give a map of the species and their relative concentrations. The model shows that (Pden)4(bipy)4 is the single most abundant species between pH = 4 and 7 and a Pden:bipy ratio of 1:0.4 to 1:6. Under optimum conditions, (Pden)4(bipy)4 holds a maximum of -80 % of the total Pd in solution when the total [Pd] = 1 x 10-5 M. The apparent equilibrium constants for 2.(Pden)(bipy)2 = (Pden)2(bipy)3+bipy and 4.(Pden)(bipy) = (Pden)4(bipy)4 were -0.6 and --106, respectively, at Pden:bipy = 1:1 and pH = 7. The model also permits analysis of the relative rates of formation of (Pden)4(bipy)4 from a number of different precursors. The dominant stepwise processes for the formation of (Pden)4(bipy)4 are dimerization of (Pden)2(bipy)2, addition of Pden to (Pden)3(bipy)4 and addition of (Pden)2(bipy) to (Pden)2(bipy)3. Other possible pathways to (Pden)4(bipy)4 involve less abundant species so are disfavored. Lipophilic derivatives of Pden (PdenR) were synthesized from 1-bromodecane or 1-bromohexadecane and solketal in 30 % and 23 % overall yield, respectively. The complex PdenR was reacted with bipy in acetonitrile and the resultant solution was then tested for ion channel activity using the bilayer clamp experiment. The decyl derivative (R = C10H21) was inactive but a range of activity which include erratic behaviors, short openings and Iong openings were observed for the hexadecyl derivative (R = C16H33) using the bilayer clamp technique. Erratic openings were observed before all short and long openings, but were also observed independently. Hille pore radii, calculated from the observed conductances, were between ˜ 1 and 6.5 Å for the rare short openings. The Hille radii for long opening pores were between ˜1 and 14 Å and these pores did not show any ion selectivity. Channels that exhibit long opening activity were also observed in the absence of Pden:bipy. The large Hille radii and activity in the absence of bipy indicate that the proposed (PdenR)4(bipy)4 channel did not form possibly because the local concentration of bipy was not high enough to compete with the lipid for coordination sites on PdenR. The implications of these findings for self-assembly of ion channels in lipid bilayer membranes are discussed.

This Thesis presents the synthesis, characterization and mechanistic explorations into a series of diphenylacetylene-containing oligoester ion channels. Eighteen final compounds were synthesized and tested for ion transport activity utilizing both vesicle and planar bilayer assays. The oligomers varied in length, hydrophobicity and the nature of the aromatic moiety. Compounds incorporating a modified diphenylacetylene (‘Dip’), or a novel phenyl-extended fluorophore (‘Trip’) were made using a reliable, modular synthesis. The final compounds were prepared in a total of 5 to 11 steps from commercial materials in yields ranging from 10 to 40%. The compounds’ activity varied considerably; both highly active and completely inactive compounds were discovered. The differences in activity are controlled by structure via the influence of structural variables on the aqueous phase aggregation and the ability of the compound to insert into the bilayer membrane. These structure-activity studies uncovered two highly-active ion transporters, HO2C-Hex-Dip-Hex-Hex-OH and –OPO32- (Hex = 6-hydroxyhexanoyl) which exhibited activity almost 10-fold higher than the fully-saturated oligoesters developed in previous work. In some cases, the transport activity is initially high but declines over a period of 20-30 minutes following compound addition. This suggests that the compound slowly transitions to an environment where it cannot form active channels. In the bilayer clamp, a variety of behaviours including highly-conducting openings were observed. An apparent voltage-gated response was exhibited by one of the Trip compounds (HO2C-Trip-G(E3)-OH), a property rarely seen for synthetic ion channels. The Dip and Trip molecules exhibited environment-sensitive fluorescence. The observed Dip excimer-like emission is the second reported instance of this in solution. The Trip compounds are solvatochromic; this property was used to infer their location in the membrane. Partitioning into the membrane was followed by a blue-shifting and increased intensity of the fluorescence emission for both series of compounds. For the Trip isomers, which are significantly more emissive than the Dip molecules, this enhancement in intensity could be visualized by eye. For the Dip oligomers, the excimer emission is a broad band with variable shape and intensity; it is time-dependent under some conditions. The excimer emission has a sub-nanosecond lifetime in homogenous solution that is significantly prolonged in the presence of vesicle bilayers, in which a number of lifetimes could be detected. Both monomer and excimer emissions can be quenched by aqueous copper, the excimer emission is more efficiently quenched than is the monomer. The photophysical characteristics of these molecules allowed for a variety of experiments designed to probe their membrane partitioning and localization behaviours. The results indicate the formation of a complex mixture of interconverting monomeric and aggregate species as the compounds move from water to the bilayer. The slow evolution of the mixture is consistent with the times noted for loss of membrane activity in transport assays. From these data a new model that describes the transport process is proposed. The key feature of this model is that transport must occur via a species that forms quickly upon the mixing of the components. Possible structures of the intermediates formed are discussed. / Graduate

Torpedo AChR structure was used to make models of other LGICs. Coarse-grain MD allowed the identification of residues in the TM domain interacting with the lipid-bilayer. Born energy profiles through LGIC pores reveal that the EC domain plays a key role in ion selectivity.

The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity. Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. Firstly, by applying a membrane potential, initial stages of the closing of the channel were captured, manifested in a secondary-structure change in the voltage-sensor. In a follow-up study, we found that the energetic cost of translocating this 310-helix conformation was significantly lower than in the original conformation. Thirdly, collaborators of ours identified new molecular constraints for different states along the gating pathway. We used those to build new protein models that were evaluated by simulations. All these results point to a gating mechanism where the S4 helix undergoes a secondary structure transformation during gating. These simulations also provide information about how the protein interacts with the surrounding membrane. In particular, we found that lipid molecules close to the protein diffuse together with it, forming a large dynamic lipid-protein cluster. This has important consequences for the understanding of protein-membrane interactions and for the theories of lateral diffusion of membrane proteins. Further, simulations of the simple ion channel antiamoebin were performed where different molecular models of the channel were evaluated by calculating ion conduction rates, which were compared to experimentally measured values. One of the models had a conductance consistent with the experimental data and was proposed to represent the biological active state of the channel. Finally, the underlying methods for simulating molecular systems were probed by implementing the CHARMM force field into the GROMACS simulation package. The implementation was verified and specific GROMACS-features were combined with CHARMM and evaluated on long timescales. The CHARMM interaction potential was found to sample relevant protein conformations indifferently of the model of solvent used. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

Mechanosensitive (MS) channels are a class of ion channels which are gated by membrane stretch. The mechanosensitive channel of large conductance (MscL) of the bacterium E.coli has become a prototype MS channel for studying structure-function relationships in this class of ion channels. MscL homologues have commonly been found in Gram-negative and Gram-positive bacterial strains forming a sub-family of a larger family of MS class of ion channels encompassing prokaryotes (bacteria and archaea) as well as cell-walled eukaryotes (fungi and plants). MscL and its homologues have been found to play an important role in osmoregulation of bacterial cells. Though the MS channels of bacteria have been thoroughly studied, little is known about the pharmacology of these channels. This thesis has one general aim, that is, to identify compounds which are able to gate and/or alter the gating of the MS channels of bacteria in particular, the MscL of E. coli. Using the patch-clamp technique, potential compounds mostly identified via in-silico techniques were examined to observe the effects on MscL reconstituted in artificial lipid membranes and MscS in giant bacterial spheroplasts. The compounds were tested for the ability to spontaneously gate the MscL and MscS and/or alter the Boltzmann distribution parameters of the MscL, indicative of an effect on the gating of MscL. Compounds showing potential as MscL activators were then examined for in-vivo effects using different growth assays. The effects of parabens, gallates, eriochrome cyanine R, brilliant green, deoxycholic acid are reported. Of these compounds, parabens and eriochrome cyanine R showed the most encouraging results. Identification of MS channel gate ligands not only benefits structural studies as tetrodotoxin has for the voltage-sensitive sodium channel, these compounds could also V potentially serve as base compounds for novel antibiotics which would target the MS channels of bacteria. Since the MS channels of bacteria serve as safety valves for the bacterium, gating during exposure to a hypo-osmotic challenge such as rain to release excessive cellular turgor, a pharmacological agent that could impair the gating of the MS channels releasing essential cytoplasmic osmolytes, would cause the growth impairment or death of the bacterium. With the rise in multi-drug resistant bacteria, continual development of novel antibiotics is crucial.

Thesis (Ph. D.)--Ohio State University, 2007. / Full text release at OhioLINK's ETD Center delayed at author's request

Thesis (Ph.D.)--McMaster University, 2004. / Supervisor: Michael J. O'Donnell. Includes bibliographical references (leaves 193-208).

Thesis (Ph. D.)--University of Hong Kong, 2008. / Includes bibliographical references (leaves 169-208) Also available in print.