TY - JOUR
T1 - Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels
AU - Robertson, J. L.
AU - Palmer, L. G.
AU - Roux, B.
N1 - Funding Information:
J.L.R. was supported by the National Science and Engineering Research Council postgraduate doctoral scholarship from Canada. This work was supported by National Institutes of Health grants GM062342 (to B.R.) and DK27847 (to L.G.P.). Computational resources were provided by the National Center for Supercomputing Applications through grant MCA01S018.
PY - 2012/8/8
Y1 - 2012/8/8
N2 - Inward rectifier potassium (Kir) channels act as cellular diodes, allowing unrestricted flow of potassium (K+) into the cell while preventing currents of large magnitude in the outward direction. The rectification mechanism by which this occurs involves a coupling between K+ and intracellular blockers - magnesium (Mg2+) or polyamines - that simultaneously occupy the permeation pathway. In addition to the transmembrane pore, Kirs possess a large cytoplasmic domain (CD) that provides a favorable electronegative environment for cations. Electrophysiological experiments have shown that the CD is a key regulator of both conductance and rectification. In this study, we calculate and compare averaged equilibrium probability densities of K+ and Cl- in open-pore models of the CDs of a weak (Kir1.1-ROMK) and a strong (Kir2.1-IRK) rectifier through explicit-solvent molecular-dynamics simulations in ∼1 M KCl. The CD of both channels concentrates K+ ions greater than threefold inside the cytoplasmic pore while IRK shows an additional K+ accumulation region near the cytoplasmic entrance. Simulations carried out with Mg2+ or spermine (SPM4+) show that these ions interact with pore-lining residues, shielding the surface charge and reducing K+ in both channels. The results also show that SPM4+ behaves differently inside these two channels. Although SPM4+ remains inside the CD of ROMK, it diffuses around the entire volume of the pore. In contrast, this polyatomic cation finds long-lived conformational states inside the IRK pore, interacting with residues E224, D259, and E299. The strong rectifier CD is also capable of sequestering an additional SPM4+ at the cytoplasmic entrance near a cluster of negative residues D249, D274, E275, and D276. Although understanding the actual mechanism of rectification blockade will require high-resolution structural information of the blocked state, these simulations provide insight into how sequence variation in the CD can affect the multi-ion distributions that underlie the mechanisms of conduction, rectification affinity, and kinetics.
AB - Inward rectifier potassium (Kir) channels act as cellular diodes, allowing unrestricted flow of potassium (K+) into the cell while preventing currents of large magnitude in the outward direction. The rectification mechanism by which this occurs involves a coupling between K+ and intracellular blockers - magnesium (Mg2+) or polyamines - that simultaneously occupy the permeation pathway. In addition to the transmembrane pore, Kirs possess a large cytoplasmic domain (CD) that provides a favorable electronegative environment for cations. Electrophysiological experiments have shown that the CD is a key regulator of both conductance and rectification. In this study, we calculate and compare averaged equilibrium probability densities of K+ and Cl- in open-pore models of the CDs of a weak (Kir1.1-ROMK) and a strong (Kir2.1-IRK) rectifier through explicit-solvent molecular-dynamics simulations in ∼1 M KCl. The CD of both channels concentrates K+ ions greater than threefold inside the cytoplasmic pore while IRK shows an additional K+ accumulation region near the cytoplasmic entrance. Simulations carried out with Mg2+ or spermine (SPM4+) show that these ions interact with pore-lining residues, shielding the surface charge and reducing K+ in both channels. The results also show that SPM4+ behaves differently inside these two channels. Although SPM4+ remains inside the CD of ROMK, it diffuses around the entire volume of the pore. In contrast, this polyatomic cation finds long-lived conformational states inside the IRK pore, interacting with residues E224, D259, and E299. The strong rectifier CD is also capable of sequestering an additional SPM4+ at the cytoplasmic entrance near a cluster of negative residues D249, D274, E275, and D276. Although understanding the actual mechanism of rectification blockade will require high-resolution structural information of the blocked state, these simulations provide insight into how sequence variation in the CD can affect the multi-ion distributions that underlie the mechanisms of conduction, rectification affinity, and kinetics.
UR - http://www.scopus.com/inward/record.url?scp=84864652652&partnerID=8YFLogxK
U2 - 10.1016/j.bpj.2012.06.023
DO - 10.1016/j.bpj.2012.06.023
M3 - Article
C2 - 22947859
AN - SCOPUS:84864652652
VL - 103
SP - 434
EP - 443
JO - Biophysical Journal
JF - Biophysical Journal
SN - 0006-3495
IS - 3
ER -