Title: K⁺ block is the mechanism of functional asymmetry in bacterial Na_v channels

Abstract

Crystal structures of several bacterial Na_v channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Na_v channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial Na_vAb channel. This approach provided new insight into the mechanism of selective ion permeation in bacterial Nav channels. The non-equilibrium simulations indicate that two or three extracellular K⁺ ions can block the entrance to the selectivity filter of Na_vAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K+ ions that can be ‘locked’ in place bymodest applied forces. In contrast to K⁺, three Na⁺ ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similarmore » local minimum in the two-dimensional free-energy landscape of two Na⁺ ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K⁺ block is equivalent to large applied potentials experimentally measured for two bacterial Na_v channels to induce inward currents of K⁺ ions. Here, these results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free-energy landscapes.« less

Authors:

Ngo, Van ^[1]; Wang, Yibo ^[2]; Haas, Stephan ^[3]; Noskov, Sergei Y. ^[2]; Farley, Robert A. ^[3]; Weinstein, Harel ^[4]

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+ Show Author Affiliations

1. Univ. of Southern California, Los Angeles, CA (United States); Univ. of Calgary, Calgary, AB (Canada)
2. Univ. of Calgary, Calgary, AB (Canada)
3. Univ. of Southern California, Los Angeles, CA (United States)
4. Weill Medical College of Cornell Univ., Ithaca, NY (United States)

Publication Date:

Mon Jan 04 00:00:00 EST 2016

Research Org.:

Univ. of Southern California, Los Angeles, CA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1242974

Grant/Contract Number:  

FG03-01ER45908

Resource Type:

Accepted Manuscript

Journal Name:

PLoS Computational Biology (Online)

Additional Journal Information:

Journal Name: PLoS Computational Biology (Online); Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1553-7358

Publisher:

Public Library of Science

Country of Publication:

United States

Language:

English

Subject:

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; potassium; potassium channels; sodium; membrane potential; biochemical simulations; oxygen; relaxation time; crystal structure