Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 103-117).

Glutamate is the major excitatory neurotransmitter in the mammalian brain. It binds to three different subclasses of ionotropic glutamate receptors (iGluRs): AMPA, kainate and NMDA receptors, and triggers a cation influx that generates synaptic currents crucial to brain function. Significantly, iGluRs are implicated in various neurological disorders, such as depression, schizophrenia, Alzheimer’s and Parkinson’s diseases, autism, seizure, and stroke. Several crystal structures for intact iGluRs in various functional states (i.e. closed, activated and desensitized) have now been reported. The receptors have also been studied using single-particle cryo-electron microscopy. Together, these studies provide fascinating ‘snap-shots’ of the receptors as they transition between different states. What is lacking, so far, is information about the kinetics underlying these structural transitions, because the techniques used lack time resolution. I have used fast-scan atomic force microscopy (AFM), in some cases in combination with UV photolysis of caged L-glutamate, to study activation-induced structural changes in GluK2 kainate receptors and GluA2 AMPA receptors. AFM provides single-molecule resolution under fluid, permitting the imaging of proteins ‘in action’. Receptors were purified from transfected cells by immunoaffinity chromatography and imaged after integration into supported lipid bilayers. Activation of both receptors caused a rapid ~1-nm vertical compression of the receptor. In both cases, the height reduction did not occur in the presence of receptor antagonists. Further, the D776K mutant of the kainate receptor, which does not desensitize, did not undergo the height change, and cyclothiazide, which blocks desensitization of the AMPA receptor, also blocked the height change. I conclude, therefore, that the vertical compression is associated with receptor desensitization, and suggest that it may reflect a weakening of the interaction between receptor subunits at the LBD dimer interface. When imaged from the ‘top’ by AFM, the receptors appeared as double-blob structures, with each blob representing a pair of ATDs. By measuring the distance between the centres of the blobs in successive AFM images, I was able to monitor the mobility of the ATDs relative to each other before and during receptor stimulation. I found that for both kainate and AMPA receptors, the relative mobility of the ATDs became greater after stimulation. Further, at low glutamate concentrations, the ATDs of the (rapidly desensitizing) flop splice variant of the AMPA receptor were more mobile than those of the (more slowly desensitizing) flip splice variant. I suggest that the greater mobility of the flop splice variant might be connected with its more short-lived functional response to activation. In a final series of experiments, in collaboration with two other groups, I used AFM to measure conformational changes induced by allosterically-bound halide ions. We found that anion substitution (i.e. chloride to bromide, or chloride to iodide) produced vertical compression of AMPA receptors prior to agonist binding, and also (in electrophysiological experiments conducted by collaborators) altered the duration of agonist-evoked channel activity. The anion binding site was identified (in X-ray crystal structures obtained by collaborators) within the ligand binding domain, where flip-flop alternative splicing occurs. Interestingly both anion effects were isoform-dependent.

The pentameric ligand gated ion channel super family plays a central role in fast synaptic communication between neurons and at the neuromuscular junction. Extensive studies on the prototypic pLGIC, the Torpedo nicotinic acetylcholine receptor (nAChR) have revealed an exquisite lipid sensitivity, with the nAChR adopting a novel uncoupled conformation in membranes lacking activating anionic and neutral lipids. The lipid-exposed transmembrane alpha-helix, M4, in each homologous subunit likely acts as a lipid sensor. One model proposes that activating lipids promote M4 “binding” to the adjacent alpha-helices, M1 and M3, to enhance interactions between the M4 C-terminus and the Cys-loop of the agonist-binding domain, with such interactions promoting coupling between the agonist site and channel gate. The first part of my thesis indirectly tests this hypothesis by exploring the effects of membrane hydrophobic thickness on nAChR function. Specifically, I tested the hypothesis that thicker membranes, which should promote alignment of M4 parallel to M1/M3 and thus helix-helix interactions, favor a coupled conformation. Although I found that the nAChR is uncoupled in all membranes tested, regardless of hydrophobic thickness, thicker membranes promote transitions from uncoupled to ultimately the desensitized state over the minutes to hours time frame. In contrast to anionic lipids, which influence function primarily via a conformational selection mechanism, membrane hydrophobic thickness influences function via a kinetic mechanism - thick membranes lower the activation energy between uncoupled and coupled conformations to promote conformational transitions. In the second part of my thesis, I used the two prokaryotic homologs, GLIC and ELIC, to explore how amino acid interactions at the interface between M4 and M1/M3 influence channel activity. Alanine scanning mutagenesis of this interface shows that disruption of almost any interaction in GLIC leads to a loss of folding and/or function, while analogous mutations in ELIC typically lead to no change or produce gains in function. Sequence comparisons with other members of the pLGIC superfamily suggest that the transmembrane domains of GLIC and ELIC represent two distinct archetypes. Each archetype may strike a different balance between the need for strong M4 binding to M1/M3 to promote folding and pentamer assembly, and the need for weaker interactions that allow for greater conformational flexibility during function.

The transient receptor potential (TRP) are cation channels mostly permeable to both monovalent and divalent cations. ThermoTRP is a specific group of directly thermally activated TRP channels. The vanilloid transient receptor potential 3 (TRPV3) is an ion channel widely expressed in keratinocytes, that is implicated in the regulation of skin homeostasis, thermo- sensing, nociception and development of itch sensation. Our results show the importance of the cytoplasmic inter-subunit interface in the heat sensitivity of TRPV3. As there is a structural analogy within the vanilloid receptors, our hypothesis of the identified important region is supposed to be valid also for other thermally activated TRPV receptors (TRPV1, TRPV2 and TRPV4). We have proved that TRPV3 is a substrate for ERK1/2 protein kinase (kinase regulated by extracellular signal 1 and 2) and we have identified TRPV3 phosphorylation sites that may be direct targets for ERK1/2. Of these residues, threonine 264 has been shown to be the main phosphorylation site responsible for TRPV3 sensitization mediated by ERK kinase. In human keratinocytes, the phosphorylation might be physiologically and pathophysiologically important in processes of TRPV3 sensitization mediated by MAPK signaling pathway. The transient receptor potential ankyrin 1...

In this study, the single-cell relative quantitative mRNA expression of three Calcium-binding proteins (CaBPs; calbindin, calretinin, parvalbumin) and eight nicotinic acetylcholine receptor (nAChR) subunits (alpha2-alpha5, alpha7, beta2-beta4) from interneurons from the stratum radiatum or stratum oriens within the CA1 region of rat hippocampi was analyzed using quantitative real time RT-PCR. Eighty-seven percent of the interneurons examined expressed CaBP mRNA. Parvalbumin mRNA was detected in 64%, while calbindin and calretinin expression was detected in 26% and 40% of interneurons, respectively. CaBP expression was not exclusive; the average number of CaBP mRNA detected per interneuron of the 47 interneurons examined for CaBP was 1.3. There was no significant difference between the proportion of CaBPs expressed in the stratum radiatum compared to the stratum oriens. However, interneurons from the stratum radiatum expressed significantly higher relative levels of mRNA for calbindin. Eighty-four percent of the 31 interneurons examined for both CaBP and nAChR subunits expressed nAChR subunit mRNA; the average number of nAChR subunits detected per interneuron was 2.9. Furthermore, of the 24, 140, and 168 possible combinations of 2-, 3-, and 4-way co-expression between CaBP+nAChR mRNA, respectively, only two significant 3-way combinations were detected: parvalbumin+a3+a5 and parvalbumin+alpha5+beta4. This study reports that subpopulations of nAChR-containing interneurons defined by quantitative CaBP mRNA expression or CaBP+nAChR co-expression do exist within the CA1 region of the hippocampus.

No description available.

<p> Potassium channels allow selective flow of K+ ions across impermeable membranes. They switch between closed and open states in response to stimulus. The closed state of KcsA, a potassium channel from the bacteria streptomyces lividans, has been crystallized and studied. However, attempts to obtain a structural description of gating transition of the channel have been hampered because the open state is transiently occupied. In this study, we investigated changes in gating functions of KcsA caused by variations in environmental parameters such as pH, voltage and also mutation in KcsA using planar bilayer and patch clamp channel recording techniques to improve our understanding on the functional aspect of gate activation of KcsA.</p> / Thesis / Master of Science (MSc)

Honey bees are economically important pollinators of a wide variety of crops that have attracted the attention of both researchers and the public alike due to unusual declines in the numbers of managed colonies in some parts of the world. Viral infections are thought to be a significant factor contributing to these declines, along with exposure to agricultural and apicultural pesticides, but viruses have proven a challenging pathogen to study in a bee model and interactions between viruses and the bee antiviral immune response remain poorly understood. Recent studies have demonstrated an important role for inwardly-rectifying ATP-sensitive potassium (KATP) channels in the cardiac regulation of the fruit fly antiviral immune response, but no information is available on their role in the heart-specific regulation of bee immunity. The results of this work demonstrate that KATP channel modulators have an observable effect on honey bee heart rate that supports their expected physiological role in bee cardiac function. Here, it is also reported that the entomopathogenic flock house virus (FHV) infects adult bees, causing rapid onset of mortality and accumulation of viral RNA. Furthermore, infection-mediated mortality can be altered by pre-exposure to KATP channel modulators. Finally, this work shows that exposure to environmental stressors such as commonly used in-hive acaricides can impact bee cardiac physiology and tolerance to viral infection. These results suggest that KATP channels provide a significant link between cellular metabolism and the antiviral immune response in bees and highlight the significant impact of environmental stressors on pollinator health. / Ph. D.

Chemical reactions involving small number of reacting molecules are noisy processes. They are simulated using stochastic simulation algorithms like the Gillespie SSA, which are valid when the reaction environment is well-mixed. This is not the case in reactions occuring on biological media like cell membranes, where alternative simulation methods have to be used to account for the crowded nature of the reacting environment. Ion channels, which are membrane proteins controlling the flow of ions into and out of the cell, offer excellent single molecule conditions to test stochastic simulation schemes in crowded biological media. Single molecule reactions are of great importance in determining the functions of biological molecules. Access to their experimental data have increased the scope of com-putational modeling of biological processes. Recently, single molecule experiments have revealed the non-Markovian nature of chemical reactions, due to a phenomenon called `dynamic disorder', which makes the rate constants a deterministic function of time or a random process. This happens when there are additional slow scale conformational transitions, giving the molecule a memory of its previous states. In a previous work, the hTREK1 two pore domain potassium channel was revealed to have long term memory in its kinetics, prompting alternate non-Markovian schemes to analyze its gating. Traditionally, ion channel gating is modeled as Markovian transitions between fixed states. In this work, we have used single channel data from hTREK1 ion channel and have provided a simple diffusion model for its gating. The main assumption of this model is that the ion channel diffuses through a continuum of states on its potential energy landscape, which is derived from the steady state probability distribution of ionic current recorded from patch clamp experiments. A stochastic differential equation (SDE) driven by Gaussian white noise is proposed to model this motion in an asymmetric double well potential. The method is computationally very simple and efficient and reproduces the amplitude histogram very well. For the case when ligands are added, leading to incorporation of long term memory in the kinetics, the SDE is modified to run on coloured noise. This has been done by introducing an auxiliary variable into the equation. It has been shown that increasing the noise correlation with ligand concentration improves the fits to the experimental data. This has been validated for several datasets. These methods are more advantageous for simulation than the Markovian models as they are true to the physical picture of gating and also computationally very efficient. Reproducing the whole raw data trace takes no more than a few seconds with our scheme, with the only input being the amplitude histogram and four parameters. Finally a quantitative model based on a modified version of the Chemical Langevin equation is given, which works on random rate parameters. This model is computationally simple to implement and reproduces the catalytic activity of the channel as a function of time. From the computational analysis undertaken in this work, we can infer that ion channel activity can be modeled using the framework of non-Markovian processes, lending credence to the recent understanding that single molecule reactions are basically processes with long-term memory. Since the ion channel is basically a protein, we can also hypothesize that the some of the properties that make proteins so vital to living organ-isms could be attributed to long-term memory in their folding kinetics, giving them the ability to sample specific regions of their conformation space, which are of interest to biological functions.

This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research.