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Straaten, T. A. van der; Tang, John M.; Ravaioli, Umberto; Eisenberg, Robert S.; Aluru, N. R.

doi:10.1023/a:1026212825047

Cited by 35 publications

(23 citation statements)

References 72 publications

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“…In our approach, we assume that beyond a Debye length from the membrane the electrostatic potential and ion densities do not vary appreciably. This assumption has been supported by the results of continuum results presented earlier [35]. For typical salt concentrations used in ion channel simulations, the Debye length is of the order of 10 Å.…”

Section: Computational Issuessupporting

confidence: 69%

Simulation of charge transport in ion channels and nanopores with anisotropic permittivity

et al. 2009

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Ion channels are part of nature's solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as largescale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and ParticleParticle-Particle-Mesh (P 3 M) methodologies developed at the University of Illinois at UrbanaChampaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters.

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Section: Computational Issuessupporting

confidence: 69%

Simulation of charge transport in ion channels and nanopores with anisotropic permittivity

et al. 2009

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“…Previously, PROPHET has been used extensively in the modeling and simulation of semiconductor-based processes (15) and devices (16). It has recently been applied to solving coupled PoissonNernst-Planck equations in the modeling of charge transport in ompF porin ion channels (17). In the current case, the interior of protein and membrane are not accessible to the electrolytes.…”

Section: Theoretical Modelsmentioning

confidence: 99%

Prediction of protein orientation upon immobilization on biological and nonbiological surfaces

Talasaz

Nemat‐Gorgani

Liu

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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We report on a rapid simulation method for predicting protein orientation on a surface based on electrostatic interactions. New methods for predicting protein immobilization are needed because of the increasing use of biosensors and protein microarrays, two technologies that use protein immobilization onto a solid support, and because the orientation of an immobilized protein is important for its function. The proposed simulation model is based on the premise that the protein interacts with the electric field generated by the surface, and this interaction defines the orientation of attachment. Results of this model are in agreement with experimental observations of immobilization of mitochondrial creatine kinase and type I hexokinase on biological membranes. The advantages of our method are that it can be applied to any protein with a known structure; it does not require modeling of the surface at atomic resolution and can be run relatively quickly on readily available computing resources. Finally, we also propose an orientation of membrane-bound cytochrome c, a protein for which the membrane orientation has not been unequivocally determined.electric double layer ͉ electrostatic simulations ͉ orientation flexibility A dsorption of proteins on solid interfaces has become an area of great theoretical and practical interest because of the recently extensive use of immobilized proteins and applications involving the catalytic potential of immobilized enzymes. Thus with the advent of protein microarrays and other solid miniaturized devices involving proteins, combined with applications in biomedical material engineering and biosensors, a greater need for defining the interactions of proteins with various surfaces has become evident. Accordingly, information on the orientation by which a protein may encounter the surface for immobilization has become an essential requirement. With such information, it would be possible to make predictions regarding details of interactions involving the participating components on the biomolecule and the reactive surface. Moreover, the residues on the biomolecule available for interaction with other proteins and ligands in solution and for binding to the reactive groups at the surface could be identified. Furthermore, customized surface chemistries resulting in a desirable immobilization orientation would become facilitated, resulting in a more targeted approach to protein immobilization.Despite the increasing need to understand how proteins attach to cellular and artificial surfaces, experimental details of the orientation by which proteins are immobilized are, to our knowledge, available only in two cases [type I hexokinase and mitochondrial creatine kinase (MtCK)] because of the difficulty in obtaining reliable experimental data. As for membrane proteins, the structure of only a limited number of cases (e.g., bacteriorhodopsin, and microsomal P450, see refs. 1 and 2) have been determined, because of the inherent difficulties associated with their crystallization. The other main stru...

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“…The electric field perpendicular to the path of the ions (i.e., parallel to the plane of the membrane) is large because the permanent charges on one side of the channel are acid (negative) and on the other side are basic (positive). 200,227,482,587,659,699,771,786,787,866,888,892 These calculations show that a single potential of mean force cannot describe the movement of ions through a channel. The path depends on the charge of the ion, and presumably (judging from other work) on its diameter, chemical interactions with the channel protein, concentration, and electrical and chemical potentials on both sides of the channel.…”

Section: µ >mentioning

confidence: 98%

Crowded Charges in Ion Channels

Eisenberg

2011

Advances in Chemical Physics

129

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Physical Chemistry and Life. Ions in water are the liquid of life. Life occurs almost entirely in 'salt water'. Life began in salty oceans. Animals kept that salt water within them when they moved out of the ocean to drier surroundings. The plasma and blood that surrounds all cells are electrolytes more or less resembling sea water. The plasma inside cells is an electrolyte solution that more or less resembles the sea water in which life began. Water itself (without ions) is lethal to animal cells and damaging for most proteins. Water must contain the right ions in the right amounts if it is to sustain life.Physical chemistry is the language of electrolyte solutions and so physical chemistry, and biology, particularly physiology, have been intertwined since physical chemistry was developed some one hundred fifty years ago. Physiology, of course, was studied by the Greeks some millennia earlier, but the biological role of electrolyte solutions could not be understood until ions were discovered by chemists some 2,000 years later.Physical chemists and biologists come from different traditions that separated for several decades as biologists identified and described the molecules of life. Communication is not easy between a fundamentally descriptive tradition and a fundamentally analytical one. Biologists have now learned to study their well defined systems with physical techniques, of considerable interest to physical chemists. Physical chemists are increasingly interested in spatially inhomogeneous systems with structures on the atomic scale so common in biology. Physical chemists will find it productive to work on well defined systems built by evolution to be reasonably robust, with input output relations insensitive to environmental insults. The overlap in science is clear. The human overlap is harder because the fields have grown independently for some time, and the knowledge base, assumptions, and jargon of the fields do not coincide. Indeed, they sometimes seem disjoint, without overlap.This article deals with properties of ion channels that in my view can be dealt with by 'physics as usual', with much the same tools that physical chemists apply to other systems. Indeed, I introduce and use a tool of physicists-a field theory (and boundary conditions) based on an energy variational approach developed by Chun Liu 141,575,766,806,944 -not too widely used among physical chemists. My goal is to provide the knowledge base, and identify the assumptions, that biologists use in studying ion channels, avoiding jargon. Although we do not know enough to write atomic, detailed physical models of the process by which ions move through channels, rather simple models of selectivity and permeation work quite well in important cases. Those physical models and cases are the main focus of this review because they demonstrate the strong essential link between the traditional treatments of ions in chemical physics, and the biological function of ion channels.At first, ion channels may seem to be an extreme system. They are as smal...

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Cited by 35 publications

References 72 publications

Simulation of charge transport in ion channels and nanopores with anisotropic permittivity

Simulation of charge transport in ion channels and nanopores with anisotropic permittivity

Prediction of protein orientation upon immobilization on biological and nonbiological surfaces

Crowded Charges in Ion Channels

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