Predicting channel function from channel structure using Brownian dynamics simulations.

S H Chung; S Kuyucak

doi:10.1046/j.1440-1681.2001.03408.x

Home/Archive/PubMed

PubMed · 11153545

Predicting channel function from channel structure using Brownian dynamics simulations.

S H Chung·S Kuyucak

View original source ↗Export metadata ↓

Abstract

1. The transport process of ions across the potassium channel is studied using computer simulations. The shape of the model channel corresponds closely to that deduced from crystallography. 2. We first give an intuitive account of how the motion of ions experiencing an applied electric force and interacting with a dielectric boundary and charge residues on the channel wall can be simulated accurately by using a powerful supercomputer. 3. We then show how some of the salient features of ion channels can be deduced by following the positions of ions at each discrete step over many millions of time steps.

Explore related subjects

Ion Transport Models, Biological Nonlinear Dynamics Potassium Channels Streptomyces Journal Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

S H Chung, S Kuyucak. Predicting channel function from channel structure using Brownian dynamics simulations.. https://doi.org/10.1046/j.1440-1681.2001.03408.x

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2001

Bundle sheath cells of small veins in maize leaves are the location of uptake from the xylem.

Rb(+) as a tracer for K(+) was used to test the hypothesis that uptake of K(+) from xylem vessels of small veins into the symplast of maize leaves occurs at the xylem/bundle sheath cell interface. 22.5 min after immersing cut leaves into 20 mM RbCl+1 mM KCl, Rb(+) appeared in the cells of the leaves. Sections of these leaves were freeze-dried. In cryo-thin sections (5 microm), (85)Rb(+) and (41)K(+) content was determined by laser microprobe mass analysis with a large resolution of about 1 microm. Determining the ratio of (85)Rb(+) to (41)K(+) in the cell walls and cytosols of bundle sheath cells, mesophyll cells, and in the cells between the xylem elements resulted in the following picture: In small veins, Rb(+) entered the symplast directly at the xylem/bundle sheath cell interface.

Ion Transport↗

PubMed1999

Proton transfer from the bulk to the bound ubiquinone Q(B) of the reaction center in chromatophores of Rhodobacter sphaeroides: retarded conveyance by neutral water.

The mechanism of proton transfer from the bulk into the membrane protein interior was studied. The light-induced reduction of a bound ubiquinone molecule Q(B) by the photosynthetic reaction center is accompanied by proton trapping. We used kinetic spectroscopy to measure (i) the electron transfer to Q(B) (at 450 nm), (ii) the electrogenic proton delivery from the surface to the Q(B) site (by electrochromic carotenoid response at 524 nm), and (iii) the disappearance of protons from the bulk solution (by pH indicators). The electron transfer to Q(B)(-) and the proton-related electrogenesis proceeded with the same time constant of approximately 100 microseconds (at pH 6.2), whereas the alkalinization in the bulk was distinctly delayed (tau approximately 400 microseconds). We investigated the latter reaction as a function of the pH indicator concentration, the added pH buffers, and the temperature. The results led us to the following conclusions: (i) proton transfer from the surface-located acidic groups into the Q(B) site followed the reduction of Q(B) without measurable delay; (ii) the reprotonation of these surface groups by pH indicators and hydronium ions was impeded, supposedly, because of their slow diffusion in the surface water layer; and (iii) as a result, the protons were slowly donated by neutral water to refill the proton vacancies at the surface. It is conceivable that the same mechanism accounts for the delayed relaxation of the surface pH changes into the bulk observed previously with bacteriorhodopsin membranes and thylakoids. Concerning the coupling between proton pumps in bioenergetic membranes, our results imply a tendency for the transient confinement of protons at the membrane surface.

Ion Transport↗

PubMed1997

Manganese uptake and toxicity in magnesium-supplemented and unsupplemented Saccharomyces cerevisiae.

The magnesium content of Saccharomyces cerevisiae was found to vary by up to fivefold at differing stages of batch growth and during growth in the presence of differing magnesium concentrations. Excess Mg was primarily sequestered in vacuoles. Mn(2+)-uptake experiments revealed that Mg-enriched cells had a markedly reduced capacity for Mn2+ accumulation. For example, after 6 h incubation in the presence of 50 microM Mn2+, Mn levels were approximately twofold higher in cells previously grown in unsupplemented medium than in those from Mg-supplemented medium. These differences were further accentuated at higher Mn2+ concentrations and were not attributable to altered cell-surface charge or altered cell-surface Mn2+ binding. Cellular Mg status also influenced Mn toxicity towards S. cerevisiae. During exposure to 5 mM Mn2+, 50% reductions in the viability of cells with initial Mg contents of approximately 1400 and 2700 nmol (10(9) cells)-1 occurred after approximately 1.6 h and 3.6 h respectively. In cells containing 3300 nmol Mg (10(9) cells)-1, more than 75% viability was still maintained after 7 h incubation with 5 mM Mn2+. It is concluded that Mn2+ uptake and toxicity in S. cerevisiae are strongly influenced by intracellular Mg, possibly through Mg-dependent regulation of divalent-cation transport activity.

Ion Transport↗