Bob Eisenberg | Rush University Medical Center (original) (raw)
Address: Chicago, Illinois, United States
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Papers by Bob Eisenberg
Biophysical Journal, 2011
Proceedings of the National Academy of Sciences, 2008
Advances in Chemical Physics, 2011
The journal of physical chemistry. B, Jan 17, 2016
The ion exchange mechanism of the sodium/calcium exchanger (NCX) crystallized by Liao et al. in 2... more The ion exchange mechanism of the sodium/calcium exchanger (NCX) crystallized by Liao et al. in 2012 is studied using the Poisson-Fermi theory developed by Liu and Eisenberg in 2014. A cycle of binding and unbinding is proposed to account for the Na(+)/Ca(2+) exchange function of the NCX molecule. Outputs of the theory include electric and steric fields of ions with different sizes, correlations of ions of different charges, and polarization of water, along with number densities of ions, water molecules, and interstitial voids. We calculate the electrostatic and steric potentials of the four binding sites in NCX, i.e., three Na(+) binding sites and one Ca(2+) binding site, with protein charges provided by the software PDB2PQR. The energy profiles of Na(+) and Ca(2+) ions along their respective Na(+) and Ca(2+) pathways in experimental conditions enable us to explain the fundamental mechanism of NCX that extrudes intracellular Ca(2+) across the cell membrane against its chemical grad...
The Journal of Chemical Physics, Jul 21, 2006
J Mol Liq, 2000
... of Physiology and Biophysics, University of Miami, School of Medicine, POBox 016430, Miami FL... more ... of Physiology and Biophysics, University of Miami, School of Medicine, POBox 016430, Miami FL 331014819 Bob Eisenberg Dept of ... McK protein seems ideally suited to provide selectivity between ions, and our preliminary analysis (in collaboration with Lesser Blum and Luigi ...
Ion channels are proteins with holes down their middle that control the flow of ions and electric... more Ion channels are proteins with holes down their middle that control the flow of ions and electric current across otherwise impermeable biological membranes. The flow of sodium, potassium, calcium (divalent), and chloride ions have been central issues in biology for more than a century. The flow of current is responsible for the signals of the nervous system that propagate over long distances (meters). The concentration of divalent calcium ions is a 'universal' signal that controls many different systems inside cells. The concentration of divalent calcium and other messenger ions has a role in life rather like the role of the voltage in different wires of a computer. Ion channels also help much larger solutes (e.g., organic acid and bases; perhaps polypeptides) to cross membranes but much less is known about these systems. Ion channels can select and control the movement of different types of ions because the holes in channel proteins are a few times larger than the (crystal radii of the) ions themselves. Biology uses ion channels as selective valves to control flow and thus concentration of crucial chemical signals. For example, the concentration of divalent calcium ions determines whether muscles contract or not. Ion channels have a role in biology similar to the role of transistors in computers and technology. Ion Channels Control Concentrations Important To Life The Way Computers Control Voltages Important To Computers.
Physical review. E, Statistical, nonlinear, and soft matter physics, 2015
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for study... more Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of polarized water molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown to be comparable to the electrical energy under physiological conditions, demonstrating the crucial role of the excluded volume of particles and the voids in the natural function of channel proteins. Water is shown to play a critical role in both correlation and steric effects in the model. We extend the classical Scharfetter-Gummel (SG) method for semiconductor devices to i...
Biophysical Journal, 2011
Proceedings of the National Academy of Sciences, 2008
Advances in Chemical Physics, 2011
The journal of physical chemistry. B, Jan 17, 2016
The ion exchange mechanism of the sodium/calcium exchanger (NCX) crystallized by Liao et al. in 2... more The ion exchange mechanism of the sodium/calcium exchanger (NCX) crystallized by Liao et al. in 2012 is studied using the Poisson-Fermi theory developed by Liu and Eisenberg in 2014. A cycle of binding and unbinding is proposed to account for the Na(+)/Ca(2+) exchange function of the NCX molecule. Outputs of the theory include electric and steric fields of ions with different sizes, correlations of ions of different charges, and polarization of water, along with number densities of ions, water molecules, and interstitial voids. We calculate the electrostatic and steric potentials of the four binding sites in NCX, i.e., three Na(+) binding sites and one Ca(2+) binding site, with protein charges provided by the software PDB2PQR. The energy profiles of Na(+) and Ca(2+) ions along their respective Na(+) and Ca(2+) pathways in experimental conditions enable us to explain the fundamental mechanism of NCX that extrudes intracellular Ca(2+) across the cell membrane against its chemical grad...
The Journal of Chemical Physics, Jul 21, 2006
J Mol Liq, 2000
... of Physiology and Biophysics, University of Miami, School of Medicine, POBox 016430, Miami FL... more ... of Physiology and Biophysics, University of Miami, School of Medicine, POBox 016430, Miami FL 331014819 Bob Eisenberg Dept of ... McK protein seems ideally suited to provide selectivity between ions, and our preliminary analysis (in collaboration with Lesser Blum and Luigi ...
Ion channels are proteins with holes down their middle that control the flow of ions and electric... more Ion channels are proteins with holes down their middle that control the flow of ions and electric current across otherwise impermeable biological membranes. The flow of sodium, potassium, calcium (divalent), and chloride ions have been central issues in biology for more than a century. The flow of current is responsible for the signals of the nervous system that propagate over long distances (meters). The concentration of divalent calcium ions is a 'universal' signal that controls many different systems inside cells. The concentration of divalent calcium and other messenger ions has a role in life rather like the role of the voltage in different wires of a computer. Ion channels also help much larger solutes (e.g., organic acid and bases; perhaps polypeptides) to cross membranes but much less is known about these systems. Ion channels can select and control the movement of different types of ions because the holes in channel proteins are a few times larger than the (crystal radii of the) ions themselves. Biology uses ion channels as selective valves to control flow and thus concentration of crucial chemical signals. For example, the concentration of divalent calcium ions determines whether muscles contract or not. Ion channels have a role in biology similar to the role of transistors in computers and technology. Ion Channels Control Concentrations Important To Life The Way Computers Control Voltages Important To Computers.
Physical review. E, Statistical, nonlinear, and soft matter physics, 2015
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for study... more Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because it includes water and calculates dielectric properties consistently as outputs. This model accounts for the steric effect of ions and water molecules with different sizes and interstitial voids, the correlation effect of crowded ions with different valences, and the screening effect of polarized water molecules in an inhomogeneous aqueous electrolyte. The steric energy is shown to be comparable to the electrical energy under physiological conditions, demonstrating the crucial role of the excluded volume of particles and the voids in the natural function of channel proteins. Water is shown to play a critical role in both correlation and steric effects in the model. We extend the classical Scharfetter-Gummel (SG) method for semiconductor devices to i...