Baron Chanda - US grants

DESCRIPTION (provided by applicant): Electrical signaling constitutes one of the primary means of communication in the central nervous system with the voltage-dependent sodium channels being responsible for initiating electrical impulses. Na+ channels exist in three functional states depending on transmembrane voltage: closed, open and inactivated. Mutations of Na+ channels that lead to incomplete inactivation has been linked to various disease conditions including congenital long QT syndrome, generalized epilepsy and muscle myotonia. Local anesthetics are a class of open channel blockers that are used to treat some channel-associated conditions and are believed to stabilize the channel in the inactivated state. The long term goal of my laboratory is to use structural approaches to understand the physical basis of gating of Na+ channels and their modulation. In this study, we propose to address a fundamental question: How do molecules like local anesthetics that bind to the channel pore modify the voltage-dependent gating behavior of ion channels. We will use fluorescence recordings of site-specific labels along with electrophysiological measurements to study the effect of local anesthetic on the conformational changes associated with voltage-sensing S4 segments of Na+ channels. We propose to study a) the effect of local anesthetic on the dynamics of individual S4 segments, b) the effect of local anesthetic on structure of the individual S4 segments, c) determine the molecular basis of coupling between S4 segments and local anesthetic binding at the pore, and d) determine if stabilizing the channel in the inactivated state favors local anesthetic binding. These experiments will be interpreted in light of the recently elucidated structure of a prototypical voltage-gated ion channel (Kv 1.2) to understand the structural basis of Na+ channel gating and its modulation by local anesthetics. PUBLIC HEALTH RELEVANCE: In order to develop better drugs to treat ion channel associated disease conditions, it becomes necessary to understand the structural underpinnings of ion channel function. The research proposed here utilizes a relatively novel structural approach to study the dynamics of the Na+ channel and its modulation by local anesthetics. This research will advance human health and well-being by contributing to the development of next generation of ion channel drugs that will modulate the channel function in a specified manner.

DESCRIPTION (provided by applicant): Ion channels directly sense a wide variety of physical and chemical stimuli. Of these, the molecular principles of temperature-sensing and temperature-dependent gating are perhaps the least understood. Here we seek to understand the molecular mechanism of temperature-sensitivity by systematically studying the engineered Shaker potassium channel. The Shaker potassium channel will be developed as a model system for biophysical studies of temperature-dependent gating because of our substantial understanding of its structure and dynamics. We propose to test the hypothesis that solvent mediated interactions of amino acid side-chains at sites undergoing a change in solvent accessibility may underlie temperature-sensitive response of ion channels. Our studies will combine newly developed free-energy measurements of channel gating with electrophysiology, fluorescence spectroscopy and molecular simulations. We will broadly focus our investigations on the voltage-sensing domain of the Shaker potassium channel. First, we will test the correlation between voltage- and temperature-sensitivity. Thermodynamic analysis of the temperature- and voltage-sensitive characteristics of the specialized temperature-sensitive ion channels led to the idea that the voltage- and temperature-sensitivities of ion channels are inversely correlated. This hypothesis will be tested by characterizing the temperature dependent response of mutants of the potassium ion channels, whose voltage-dependencies are reduced by neutralization of charge residues responsible for their voltage-dependence. Second, we will test the importance of the non-polar residues in the S4 segment of the Shaker channel and its influence on temperature sensitivity. The hydrophobic residues of S4 segment are likely to undergo a change in environment polarity as the channel activates. We will test whether altering the polarity of these sites leads to temperature-dependent phenotypes. We will also utilize heavy water as a probe for studying solvent accessibility at these sites. These experiments will be combined with novel spectroscopic approach to test whether the temperature sensitive substitutions alter the nature of structural changes occurring in the proteins. Finally, we will evaluate the importance of water-accessible residues within protein crevices. Altering the polarity of these residues is expected to change the energies associated with their solvation/desolvation process. We will introduce polar and non-polar substitutions at each of these sites and test the functional temperature sensitivity of these mutants. The effects of these substitutions on the geometry of the crevices will be assessed by measuring the ionic strength dependence of charge translocation process. These experiments will be combined with molecular dynamics simulations to evaluate the role of these perturbations on water dynamics within the crevices. At the conclusion of these studies, we would have made significant headway in testing molecular theories that may underlie the temperature-dependence of ion channel gating, developed a new model system and refined our knowledge of the role of water in ion channel gating.

DESCRIPTION (provided by applicant): The eukaryotic voltage-gated sodium channel is responsible for initiating and propagating electrical impulses in neurons and most excitable cells. They are the major targets of drugs and naturally occurring toxins that modify electrical activity and mutations of sodium channel genes have been linked to disease conditions such as congenital long QT syndrome, generalized epilepsy and muscle myotonia. Despite much progress in understanding the role of sodium channels in the human body, there remains a significant gap in our knowledge of the biophysical mechanisms that underpin sodium channel function. Very little is known about the structural rearrangements and the underlying forces that drive the gating transitions which allow the channels to open briefly in response to a change in membrane potential. Development of well-constrained structural models has been hampered both due to our inability to study the activation process in isolation and a lack of thermodynamic tools to experimentally measure molecular forces in complex proteins. Spectroscopic and functional studies with domain specific toxins have revealed that the voltage-dependent movement of domain IV in the sodium channel is slower than those of the other three domains. The central goal of this project is to test the hypothesis that asynchronous gating in voltage-gated sodium channels arises due to differences in molecular forces responsible for electromechanical coupling within each domain. This proposal is based on our recent findings that have led to the development of analytical tools to extract site-specific interaction energies n a model-independent fashion. This analysis will be combined with cysteine accessibility, voltage-clamp fluorimetry and single-channel recording studies to develop a well-constrained structurally relevant quantitative description of sodium channel gating. These studies will be conducted on an inactivation deficient mutant background to avoid any complications that arise due to overlap of the activation and inactivation process. In specific aim 1, we will develop a well-constrained kinetic model for activation of voltage-gated sodium channels. These studies are expected to reveal distinct features associated with sodium channel gating which are typically masked in the wild-type channels due to rapid entry into the inactivated state. In specific aim 2, we will determine the molecular mechanism of activation gating in eukaryotic sodium channels. These experiments will test the notion that the S6 segments grant access to the pore in these channels. Finally, in specific aim 3, we will probe the molecular basis of voltage-sensor and pore domain interactions in voltage-dependent ion channel using Generalized Interaction energy Analysis (GIA). The proposed studies are expected to shed new light on the molecular forces that underlie conformational changes during the activation of a voltage-dependent sodium channels.

Project Summary Hyperpolarization-activated and cyclic nucleotide-gated ion channels (HCN) are highly expressed in the heart and central nervous system where they responsible for slowly activating currents that contribute to pacemaking activity. In addition to their role in generating rhythmic oscillations in neuronal circuits, these channels also play a crucial role in working memory and motor learning. They are important pharmacological targets for new drug development to treat disease conditions such as epilepsies and neuropathic pain. Despite the progress in understanding the structure and physiological role of these ion channels, there remains a significant gap in our knowledge of the biophysical mechanisms that underpin HCN channel behavior. These channels are unique in the voltage-gated ion channel superfamily and have the potential to provide new insights into inward rectification and ligand activation. For instance, ensemble ligand binding measurements using patch clamp fluorimetry have recently suggested a remarkable model of ligand activation that involves a sequence of positive and negative modulation of channel activity by physiological ligand. Although numerous crystal structures of cyclic nucleotide-binding domain (CNBD) from HCN channels are available, the mechanisms that underlie this unusual form of cooperativity remain unclear. The central goal of this project is to understand how the chemical structure and the resulting forces orchestrate ligand activation in HCN channels. This proposal takes advantage of the interdisciplinary expertise at UW-Madison to combine single molecule measurements of ligand binding with structural and functional analysis of ligand activation. We will test the hypothesis that ligand activation in HCN channels may involve a symmetry-breaking switch to a dimer of dimer configuration. In specific aim 1, we will use zero-mode waveguides to measure the binding of individual ligands to the cyclic-nucleotide binding domains. This will allow us to directly measure energetics of each ligand-binding step and to track the cooperativity associated with this process. With this analysis in hand, we will be able to identify the key molecular determinants responsible for each of the four ligands. In specific aim 2, we will use X-ray crystallography to determine the structures of the unliganded states of the HCN CNBDs as well as new conformations of their liganded forms. In specific aim 3, we will carry out functional analysis of ligand activation using electrophysiological and biochemical binding studies. These studies combined with mutagenesis will identify the molecular bases for isoform-specific differences in ligand activation. The proposed studies are expected to shed new light on the molecular forces that underlie conformational changes during the ligand activation in a voltage- and ligand-activated ion channel.

Project Summary/Abstract Optogenetics encompasses a broad array of tools and techniques that involve the use of light, in conjunction with molecular genetic tools, to drive and monitor activity of specific types of excitable cells in the nervous system and heart. Compared to traditional electrophysiological techniques, these methods are far less invasive and have the potential to monitor and manipulate electrical activity at multiple sites at the same time. The promise of optogenetics is not solely limited to expanding our basic understanding of complex organ systems but will also have a profound impact on the development of new therapeutics. Despite their promise, the current generation of optogenetic actuators are inferior compared to standard electrophysiological methods. While the membrane potential in a typical electrophysiological experiment can be changed by hundreds of millivolts on a sub- millisecond timescale, the current generation of light-activated ion channels are able to drive membrane potential by only a few millivolts in a millisecond. Much of the cutting-edge development in the field has focused on modifying and reengineering naturally-occurring ion channels, but these approaches have some inherent limitations. Herein, we propose to develop a new class of synthetic probes that serve as light-activated actuators for controlling membrane potential and ion concentrations with high temporal and spatial resolution. Employing a chemical synthesis approach towards these probes will allow us much greater flexibility to engineer and design more efficient actuators having the necessary throughput to drive cellular membrane potential. In addition, these chemical ion carriers can be combined with genetically encoded light-activated probes to provide even greater flexibility. The proposed research capitalizes on the expertise of a synthetic chemist (Prof. Schomaker, UW- Chemistry) and an ion channel electrophysiologist (Prof. Chanda, UW-Neuroscience). The two specific aims will focus on: a) the design and synthesis of photoactive ionophores and ion carriers, b) Characterization of the optical and transport properties of these designer ionophores and ion carriers.

Project Summary Members of the voltage-gated ion channels (VGICs) are critical for electrical and chemical signaling throughout the three kingdoms of life. Dysfunction of ion channels underlie a wide range of pathophysiology and they are one of the primary targets for new drug development. Although they share a common membrane architecture, the channels in this superfamily exhibit surprising diversity of function. Most open in response to a membrane depolarization but some open on hyperpolarization. Many of them are also polymodal- their activity is regulated by second messengers such as cyclic nucleotide or a physical stimulus such as temperature. The main objective of this proposal is to probe the molecular driving forces in order to understand the fundamental mechanisms of voltage-gating and its modulation by temperature and ligand. Current mechanistic approach tends to be structure focused to the extent that protein dynamics is either ignored or treated as secondary. Although the structures of many highly temperature-sensitive ion channels are now available, our understanding of the mechanism of tem- perature-sensitivity remains limited, in large part, due to our inability to directly probe the molecular forces. To address this issue, we are using a multi-pronged approach that combines new and existing tools to systematically characterize the molecular interactions that determine polarity of voltage-gating, exquisite temperature-sensitiv- ity and unusual allostery in VGICs. We are using the HCN channel as a model system to study gating polarity and ligand activation. Using zero model waveguides and newly developed high-throughput analysis algorithms we were able to probe the cooperativity of ligand binding in a model system. We are now poised to extend these studies to full-length channels and receptors. With regards to mechanisms of gating polarity, we have made a surprising discovery that a bipartite switch regulates gating polarity in HCN channels. Microsecond scale simu- lations in Anton supercomputer suggest a gating model which we will be tested further. We will carry out structural studies and combine it with voltage clamp fluorometry in order to annotate these structures. Next, we will also use ancestral protein reconstruction approach, to identify the deep allosteric networks that regulate gating po- larity in these channels. Our studies on temperature-dependent gating is based on two model systems: a) Tem- perature-sensitive Shaker mutant and, b) archaeal MthK channel. In order to determine the essential elements that are responsible for ?sensing? temperature, we have to measure the thermodynamic properties such as heat capacity. We propose to develop a new approach involving single molecule force spectroscopy to extract these energetic parameters. Overall, our ?molecular forces? focused approach has the potential to provide unparalleled insights into the mechanisms of voltage gating and its regulation by temperature in VGICs.