Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session W38: Focus Session: Ion Channel Physics and Chemical Physics I |
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Sponsoring Units: DCP Chair: Rob Coalson, University of Pittsburgh Room: 410 |
Thursday, March 19, 2009 11:15AM - 11:51AM |
W38.00001: Numerical modeling of fast gate-coupled ion permeation in ClC channels Invited Speaker: We have developed a three dimensional Brownian dynamics (BD) and discrete-state model to couple ion permeation to the motion of a putative fast gate in the ClC channels. The model channel is designed so as to represent certain essential features of ClC chloride channel, in which a glutamate side chain moves from an open state to a closed state (blocking the channel pore at a position which also acts as a binding site for Cl$^{-}$ ions moving through the channel). Both BD and the discrete-state model generate results in qualitative agreement with experimental observations and consistent with the foot-in-the-door mechanism. Furthermore, we have formulated a numerical approach to calculate the discrete rate constants in our model channel using BD. The discrete-state model with the rate constants solved via BD produces results consistent with the (continuous space) multi-ion BD simulations. [Preview Abstract] |
Thursday, March 19, 2009 11:51AM - 12:27PM |
W38.00002: Modeling Ion Solvation and Transport through Chloride Transport Proteins Invited Speaker: Ion channels and transporters are membrane proteins that selectively conduct ions either passively (channels) or actively using a chemical gradient of one ion (transporters). The H+/Cl- transporter, first discovered in bacteria, has now been shown to also occur in animals and plants. This talk will discuss computational approaches aimed at understanding the ion transit pathways through the bacterial chloride transporter. A Monte Carlo method (TransPath) that uses the crystal structure as input and exhaustively searches the protein for open pore spaces and favorable electrostatic domains has been developed. The algorithm successfully predicted pathways for the motion of chloride ions and protons. In order to better understanding the free energies along the predicted transport pathways, we have developed a new statistical mechanical approach for computing absolute solvation free energies in restricted environments based on a quasi-chemical approach. Anion free energy results employing the new method will be presented. [Preview Abstract] |
Thursday, March 19, 2009 12:27PM - 1:03PM |
W38.00003: Snug-fit, fluctuations, and metal-ion hydration in the selectivity of potassium ion channels Invited Speaker: On the basis of molecular simulation, an identification of a single dominating physical factor responsible for Na+/K+ selectivity of the KcsA channel has been contentious. The potential distribution theorem and quasi-chemical theory cast new light on the factors responsible for Na+/K+ selectivity. In that context, we argue that an alternative definite formulation of the molecular statistical thermodynamic problem can help in achieving a concensus view of selectivity. We summarize the necessary new theoretical ingredients and published numerical results in working toward that concensus view. [Preview Abstract] |
Thursday, March 19, 2009 1:03PM - 1:39PM |
W38.00004: Conformation changes in the Glutamate receptor as studied by LRET Invited Speaker: Glutamate receptors are the primary mediators of excitatory neurotransmission in the mammalian central nervous system. Glutamate binding to an extracellular ligand binding domain initiates a series of conformational changes that results in the formation of cation selective transmembrane ion channels that ultimately desensitize. We have used luminescence resonance energy transfer to determine the conformational changes that underlie the allosteric process of glutamate mediated gating in the receptor. These investigations showed that agonist binding induced cleft closure in the ligand binding domain confirming that this change observed in the isolated ligand binding domain of the receptor is one of the mechanisms by which agonist mediates activation. The LRET investigations also allowed a study of the conformational changes between the subunits. The apo state of the protein showed a dimer interface that was open. The dimer interface was brought together only in the activated state, suggesting that cleft closure drives the formation of the contacts at dimer interface, which in turn transiently stabilizes the open channel. At longer times, the stress induced by the transmembrane segments, ultimately drives the breakdown of the interface, leading to channel closure and receptor desensitization. [Preview Abstract] |
Thursday, March 19, 2009 1:39PM - 1:51PM |
W38.00005: Electric and Molecular Characteristics of Ion Channels Richard DeSantis A galvanic cell's electrolyte is an insulator. A conductive electrolyte would quickly discharge a dry cell's voltage. Voltage-producing paths within an electrolyte can develop spontaneously. A voltage-producing path must bridge from the anode to the cathode, to export voltage out of the insulating electrolyte. Doubling cathode to anode distance does not decrease the cell's fixed output voltage. The fixed voltage indicates superconductor-like behavior. Gaps between voltage-producing molecules would isolate the anode from the cathode, preventing superconductor-like behavior. Gating activity within membrane protein complexes can prevent or allow voltage-producing paths. A voltage-producing path is a single molecule containing both anode and cathode reactants. Only combined anode-cathode reactions within a single molecule can produce the cell's fixed exterior voltage. While within the single molecule, atoms can relocate and react. In a lead acid cell, charging voltage raises the molecule's energy state. The extra energy allows Pb and PbO2 to form during the molecule's collapse. For discharging, an external circuit provides an outlet for the molecule's voltage, which lowers the molecule's energy state to a level that permits PbSO4 production. [Preview Abstract] |
Thursday, March 19, 2009 1:51PM - 2:03PM |
W38.00006: Coulombic dragging of molecular assemblies on nanotubes Petr Kral, Kyaw Sint, Boyang Wang We show by molecular dynamics simulations that polar molecules, ions and their assemblies could be Coulombically dragged on the surfaces of single-wall carbon and boron-nitride nanotubes by ionic solutions or individual ions moving inside the nanotubes [1,2]. We also briefly discuss highly selective ionic sieves based on graphene monolayers with nanopores [3]. These phenomena could be applied in molecular delivery, separation and desalination.\\[3pt] [1] Boyang Wang and Petr Kral, JACS 128, 15984 (2006). \\[0pt] [2] Boyang Wang and Petr Kral, Phys. Rev. Lett. 101, 046103 (2008). \\[0pt] [3] Kyaw Sint, Boyang Wang and Petr Kral, JACS, ASAP (2008). [Preview Abstract] |
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