Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods

Mamonov, Artem B.; Kurnikova, Maria; Coalson, Rob D.

doi:10.1016/j.bpc.2006.03.019

Cited by 78 publications

(134 citation statements)

References 41 publications

(74 reference statements)

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“…To validate the Bayesian scheme, we first consider a comparison to the MSD method37, which is simpler, but of more limited applicability. The latter method, the results of which are shown as filled symbols in Fig.…”

Section: Resultsmentioning

confidence: 99%

Subdiffusion in Membrane Permeation of Small Molecules

Chipot

Comer

2016

Sci Rep

133

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Within the solubility–diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.

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Section: Resultsmentioning

confidence: 99%

Subdiffusion in Membrane Permeation of Small Molecules

Chipot

Comer

2016

Sci Rep

133

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“…32,50 ΔW is the free energy difference between the barrier and the well. K b and K w are the curvatures of the barrier and well, respectively.…”

Section: ■ Methodsmentioning

confidence: 99%

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

2014

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A recent crystallization of several ion channels has provided strong impetus for efforts aimed at understanding the different strategies employed by nature for selective ion transport. In this work, we used two variants of the selectivity filter of NaK channel to explore molecular mechanisms that give rise to K(+)-selectivity. We computed one-dimensional (1D) and two-dimensional (2D) potentials of mean force (PMFs) for ion permeation across the channel. The results indicate that the energies for Na(+) and K(+) permeation across the selectivity filter display significant differences in positions of the binding sites and barriers. One characteristic signature of a K(+)-selective channel is the apparent preservation of the site analogous to that of S2 in KcsA. The S2-bound ion can be almost ideally dehydrated and coordinated by 6 to 8 carbonyls. In a striking contrast, the PMFs controlling transport of ions in a nonselective variant show almost identical profiles for either K(+) or Na(+) and significant involvement of water molecules in ion coordination across the entire selectivity filter. An analysis of differences in 1D PMFs for Na(+) and K(+) suggests that coordination number alone is an insufficient predictor of site selectivity, while chemical composition (ratio of carbonyls and water molecules) correlates well with preference for K(+). Multi-ion effects such as dependence of the barriers and wells for permeant ion on the type of copermeant ion were found to play a significant role in the selectivity signature of the channel as well.

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“…Since our analysis here is only semi-quantitative, we did not pursue more sophisticated methods [38–42]; in principle, the transmission coefficient which depends on the rate of diffusion along the channel can be obtained more accurately.…”

Section: Theory and Methodologymentioning

confidence: 99%

Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport

Sugitani

Stuchebrukhov

2009

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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We have examined the network of connected internal cavities in cytochrome c oxidase along which water produced at the catalytic center is removed from the enzyme. Using combination of structural analysis, molecular dynamics simulations, and free energy calculations we have identified two exit pathways that connect the Mg2+ ion cavity to the outside of the enzyme. Each pathway has a well-defined bottleneck, which determines the overall rate of water traffic along the exit pathway, and a specific cooperative mechanism of passing it. One of the pathways is going via Arg 438/439 (in bovine numbering) toward the CuA center, approaching closely its His204B ligand and Lys171B residue; and the other is going toward Asp364 and Thr294. Comparison of the pathways among different aa3-type enzymes shows that they are well conserved. Possible connections of the finding to redox-coupled proton pumping mechanism are discussed. We propose specific mutations near the bottlenecks of the exit pathways that can test some of our hypotheses.

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Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods

Cited by 78 publications

References 41 publications

Subdiffusion in Membrane Permeation of Small Molecules

Subdiffusion in Membrane Permeation of Small Molecules

Molecular Strategies to Achieve Selective Conductance in NaK Channel Variants

Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport

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