The goal of this research proposal is to pursue our efforts to characterize the fundamental principles governing ion channel function from a detailed atomic and molecular perspective. The KcsA channel provides a fantastic framework for deepening our understanding of the physics of ion permeation and selectivity. This channel also exhibits a gating process involving a conformational change of the selectivity filter similar to the familiar C- type (slow) inactivation. The structures of the open KcsA with its filter in the conductive and inactivated state have now been determined by x-ray crystallography in the Perozo lab, and one can start to unravel the structural and energetic features governing this complex process using advanced computational methods. Concerning voltage gating, the structure of the Kv1.2 channel provides an excellent starting point for designing better atomic models and experiments. Furthermore, there growing body of information about numerous channels, which allows us to address several fundamental issues about permeation concerning the nature of ion diffusion through wide aqueous vestibules and its sensitivity to pore shape and electrostatics. The proposed projects are designed to address fundamental issues about ion permeation, inactivation and gating using a computational and experimental approach. We use a combination of computational (all-atom molecular dynamics simulations, potential of mean force umbrella sampling computations, Poisson-Boltzmann calculations, Brownian dynamics simulations, string method with swarms-of-trajectories) and experimental approaches (x- ray crystallography). The computational efforts are designed to help develop a coherent perspective from the (sometimes conflicting) information from the wide range of structural, biophysical and functional measurements and make experimentally testable predictions. The planned experimental investigations are directly relevant to issues raised by the modeling.
The goal of this research project is to expand our understanding of the function of ion channels at the molecular level using realistic computer simulations and experiments. Malfunction of ion channels have a broad impact on human health, including neurological disorders, epilepsia, heart arrhythmia, immune response, and cellular secretion. The fundamental knowledge gained by the proposed studies is also expected to play an important role in drug discovery and lead optimization.
|Lueck, John D; Mackey, Adam L; Infield, Daniel T et al. (2016) Atomic mutagenesis in ion channels with engineered stoichiometry. Elife 5:|
|Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan et al. (2016) Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nat Commun 7:12753|
|Kratochvil, Huong T; Carr, Joshua K; Matulef, Kimberly et al. (2016) Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science 353:1040-1044|
|Medovoy, David; Perozo, Eduardo; Roux, BenoÃ®t (2016) Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel. Biochim Biophys Acta 1858:1722-32|
|Castillo, Juan P; Rui, Huan; Basilio, Daniel et al. (2015) Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nat Commun 6:7622|
|SÃ¡nchez-RodrÃguez, Jorge E; Khalili-Araghi, Fatemeh; Miranda, Pablo et al. (2015) A structural rearrangement of the Na+/K+-ATPase traps ouabain within the external ion permeation pathway. J Mol Biol 427:1335-44|
|Gumbart, James C; Beeby, Morgan; Jensen, Grant J et al. (2014) Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. PLoS Comput Biol 10:e1003475|
|Li, Qufei; Wanderling, Sherry; Paduch, Marcin et al. (2014) Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 21:244-52|
|Tietjen, Gregory T; Gong, Zhiliang; Chen, Chiu-Hao et al. (2014) Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4. Proc Natl Acad Sci U S A 111:E1463-72|
|Weingarth, Markus; van der Cruijsen, Elwin A W; Ostmeyer, Jared et al. (2014) Quantitative analysis of the water occupancy around the selectivity filter of a K+ channel in different gating modes. J Am Chem Soc 136:2000-7|
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