Modeling of ion permeation in calcium and sodium channel selectivity filters

Ganesh, Pattan-Siddappa; Chanda, Baron; Gupta, Sagar V.; Mathew, M. K.; Chandrasekhar, Jayaraman

doi:10.1002/(sici)1097-0134(20000301)38:4<384::aid-prot4>3.0.co;2-m

Cited by 8 publications

(4 citation statements)

References 23 publications

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“…Molecular dynamics simulations using charge perturbations on the permeating ion were carried out previously for a set of glutamates projecting into a protein structure called a beta barrel, intended to simulate the calcium channel, 7 but the energies were incompatible with experiment, probably because of a lack of ions in the bath. Similar computations were performed recently by Ganesh et al, 8 using a set of four acetates to simulate the glutamates, but similarly lacked ions in the bath.…”

Section: Introductionmentioning

confidence: 81%

Monte Carlo Simulations of the Mechanism for Channel Selectivity: The Competition between Volume Exclusion and Charge Neutrality

et al. 2000

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A mechanism for selectivity of calcium over sodium in a biological channel is studied by means of a Monte Carlo simulation. This model channel is an infinite cylinder containing negatively charged glutamates, each modeled as a pair of half charged oxygens, and an electrolyte. The fluid in the channel is in equilibrium with a bulk electrolyte. The proportion of Ca 2+ ions in the channel is greatly in excess of that in the bulk because, in the restricted space in the channel, the doubly charged Ca 2+ ions require less volume and are more effective at neutralizing the charge of glutamates than twice the number of singly charged Na + ions with the same amount of charge.

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Section: Introductionmentioning

confidence: 81%

Monte Carlo Simulations of the Mechanism for Channel Selectivity: The Competition between Volume Exclusion and Charge Neutrality

et al. 2000

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“…The interacting calcium or sodium ions move simultaneously, in a coordinated manner, enabling escape to occur over a potential barriers of minimal height on the 2D potential energy surface (PES) [70,71]. The PES approach allows one to describe double-ion conduction as the potential motion of a quasiparticle along an optimal stochastic trajectory on the PES [36,46,72], thereby reducing the problem of doubleion conduction to the case already discussed, i.e., the 1D movement of a particle (in this case a "superion") in an electrostatic field.…”

Section: E Barrierless Double-ion Trajectories For Conduction Bands mentioning

confidence: 99%

Energetics of discrete selectivity bands and mutation-induced transitions in the calcium-sodium ion channels family

et al. 2013

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We use Brownian dynamics (BD) simulations to study the ionic conduction and valence selectivity of a generic electrostatic model of a biological ion channel as functions of the fixed charge Q(f) at its selectivity filter. We are thus able to reconcile the discrete calcium conduction bands recently revealed in our BD simulations, M0 (Q(f)=1e), M1 (3e), M2 (5e), with a set of sodium conduction bands L0 (0.5e), L1 (1.5e), thereby obtaining a completed pattern of conduction and selectivity bands vs Q(f) for the sodium-calcium channels family. An increase of Q(f) leads to an increase of calcium selectivity: L0 (sodium-selective, nonblocking channel) → M0 (nonselective channel) → L1 (sodium-selective channel with divalent block) → M1 (calcium-selective channel exhibiting the anomalous mole fraction effect). We create a consistent identification scheme where the L0 band is putatively identified with the eukaryotic sodium channel The scheme created is able to account for the experimentally observed mutation-induced transformations between nonselective channels, sodium-selective channels, and calcium-selective channels, which we interpret as transitions between different rows of the identification table. By considering the potential energy changes during permeation, we show explicitly that the multi-ion conduction bands of calcium and sodium channels arise as the result of resonant barrierless conduction. The pattern of periodic conduction bands is explained on the basis of sequential neutralization taking account of self-energy, as Q(f)(z,i)=ze(1/2+i), where i is the order of the band and z is the valence of the ion. Our results confirm the crucial influence of electrostatic interactions on conduction and on the Ca(2+)/Na(+) valence selectivity of calcium and sodium ion channels. The model and results could be also applicable to biomimetic nanopores with charged walls.

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“…The filter of the calcium channel contains four glutamate side chains that are attached, or tethered, to the channel wall [22]. For pH >.…”

Section: Modelmentioning

confidence: 99%

Monte Carlo study of the selectivity of calcium channels: improved geometrical model

2002

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An extended model of a calcium channel is described involving a channel with a finite length. With this new geometry the channel is still selective but less so than in an infinite cylinder geometry (, 2000, J. phys. Chem. B, 104, 8903). The selectivity of the channel depends on the width and length of the channel filter but is not significantly affected by changes in the size of the entry vestibules. Interestingly, changes in the size of the entry vestibules do affect the details of the concentration profiles of some of the ions.

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Modeling of ion permeation in calcium and sodium channel selectivity filters

Cited by 8 publications

References 23 publications

Monte Carlo Simulations of the Mechanism for Channel Selectivity: The Competition between Volume Exclusion and Charge Neutrality

Monte Carlo Simulations of the Mechanism for Channel Selectivity: The Competition between Volume Exclusion and Charge Neutrality

Energetics of discrete selectivity bands and mutation-induced transitions in the calcium-sodium ion channels family

Monte Carlo study of the selectivity of calcium channels: improved geometrical model

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