Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.
In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.
Chung
Shin-Ho
SH
Research School of Biological Sciences, Australian National University, Canberra, Australia. shin-ho.chung@anu.edu.au
Corry
Ben
B
D001426:Bacterial Proteins; D002244:Carbon / Q000737:chemistry*; D003198:Computer Simulation; D004553:Electric Conductivity; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D015640:Ion Channel Gating; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D015221:Potassium Channels / Q000737:chemistry* / Q000648:ultrastructure*; D024642:Potassium Channels, Voltage-Gated; D011487:Protein Conformation
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C504448:KcsA protein, Streptomyces coelicolor; D015221:Potassium Channels; D024642:Potassium Channels, Voltage-Gated; D002244:Carbon