Isoleucine gate blocks K+ conduction in C-type inactivation
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília, Brazil
- Department of Biochemistry and Molecular Biology, The University of Chicago, United States
- Department of Neurobiology, The University of Chicago, United States
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana−Champaign, Unité Mixte de Recherche No. 7019, Université de Lorraine, Université de Lorraine, France
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, and Department of Physics, University of Illinois at Urbana−Champaign, United States
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Chile
Figures
Figure 1
Comparative analysis of Kv channel structures.
(A) Schematic representation of a voltage-gated K+ channel undergoing C-type inactivation, whereby prolonged activation by an external voltage V leads to blockage of ionic conduction across the …
Figure 2 with 2 supplements
Molecular dynamics (MD) simulation of kv1.2-kv2.1-3m at +200 mV.
(A) Molecular representation of the main pore of the channel, highlighting the initial configuration of the selectivity filter, I398 (red) and V402 (light gray). (B and C) Analysis of AMBER and …
Figure 2—figure supplement 1
Ion conduction across the dilated conformation of the selectivity filter of kv1.2-kv2.1-3m.
(A, B) Shown are representative single-ion conduction events across the selectivity filter of the triple-mutant channel along AMBER and CHARMM36m simulations. (C) Closure of the isoleucine gate …
Figure 2—figure supplement 2
Molecular dynamics (MD) simulation of kv1.2-kv2.1-3m at +200mV.
(A) Molecular representation of the main pore of the channel, highlighting the initial configuration of the selectivity filter, I398 (red) and V402 (light gray). (B and C) Analysis of AMBER* …
Figure 3 with 5 supplements
Electrophysiology measurements of I398N substitution.
(A, B, C, and D) Macroscopic current recorded from: (A) kv1.2-kv2.1 chimera, (B) triple-mutant kv1.2-kv2.1-3m, (C) triple-mutant kv1.2-kv2.1-3m with I398N substitution, and (D) their respective …
Figure 3—figure supplement 1
Decay of the ionic current of the triple-mutant kv1.2-kv2.1-3m channel.
(A) Ionic traces from the triple-mutant channel and (B) its time constants fitted with a one exponential decay. When extrapolated to +200 mV where the simulation was performed, the time constant …
Figure 3—figure supplement 2
Estimation of the binding free energy of charybdotoxin (CTX).
(A) Docking of CTX to the selectivity filter of the kv1.2-kv2.1 chimera channel. (B) Docking solutions (light black traces) best reproducing the experimentally resolved bound state of the toxin …
Figure 3—figure supplement 3
State dependence of I398N effects.
(A) Macroscopic current from the double-mutant chimera channel kv1.2-kv2.1-2m (S367T/V377T). (B) Macroscopic current from kv1.2-kv2.1-2m with I398N substitution. Mutation I398N in the absence of …
Figure 3—figure supplement 4
Molecular dynamics (MD) simulation of kv1.2-kv2.1-3m with I398N at +200mV.
(A) Molecular representation of the main pore of the channel, highlighting the initial configuration of the selectivity filter, N398 (green) and V402 (light gray). (B and C) Analysis of AMBER and …
Figure 3—figure supplement 5
Primary-sequence conservation throughout the main-pore segments PH, SF, and S6.
(A) Logos conservation across K+ channels. (B) Multiple sequence alignment of most studied K+ channels.
Figure 4 with 3 supplements
Mechanism of C-type inactivation of the triple-mutant channel kv1.2-kv2.1-3m.
(A) Free-energy profile w(s) along the conformational transition path s connecting the conductive (s=0.2) and dilated (s=1) states of the selectivity filter. The free-energy profile is conditional …
Figure 4—figure supplement 1
Conformational path between the conductive (O) and dilated (D) states of the selectivity filter.
(A, B) Time evolution of the instantaneous (red) and target (black) root-mean-square deviation (RMSD) of the selectivity filter between states O and D. Reference structures of the dilated and …
Figure 4—figure supplement 2
Convergence analysis of free-energy calculations.
(A, B) Respectively shown is the root-mean-square deviation (RMSD) of the free-energy profiles w(s) and w(d) as a function of simulation time t.
Figure 4—figure supplement 3
Molecular dynamics (MD) simulation of kv1.2-kv2.1-3m at +200 mV and 150 mM NaCl.
(A) Molecular representation of the main pore of the channel, highlighting the initial configuration of the selectivity filter, I398 (red) and V402 (light gray). Two sodium (Na+) ions (yellow) are …
Additional files
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Supplementary file 1
Molecular dynamics (MD) simulations of triple-mutant channel kv1.2-kv2.1-3m.
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp1-v3.docx
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Supplementary file 2
NBFixes for potassium, carbonyl, and water interactions.
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp2-v3.docx
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Supplementary file 3
Number of conduction events along simulations of the open-conductive MthK.
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp3-v3.docx
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Supplementary file 4
Number of conduction events along molecular dynamics (MD) simulations in which the isoleucine gate is open.
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp4-v3.docx
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Supplementary file 5
Binding free-energy difference of charybdotoxin (CTX).
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp5-v3.docx
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Supplementary file 6
Comparative analysis of the average properties of the isoleucine gate with and without mutation (I398N).
- https://cdn.elifesciences.org/articles/97696/elife-97696-supp6-v3.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/97696/elife-97696-mdarchecklist1-v3.pdf
