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Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation.

Camacho CJ - PLoS ONE (2008)

Bottom Line: If the membrane potential is hyperpolarized, essential dynamics further suggests that the T1 domain returns to a configuration where the peptide is un-stretched and the S1-T1 linker is extended.Coupling this novel hyperpolarized substate to the closed, open and blocked pore states is enough to quantitatively estimate the number of open channels as a function of time and membrane potential.A straightforward prediction of the model is that a slow ramping of the potential leads to very small currents.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. ccamacho@pitt.edu

ABSTRACT
Ion channels play a central role in setting gradients of ion concentration and electrostatic potentials, which in turn regulate sensory systems and other functions. Based on the structure of the open configuration of the Kv1.2 channel and the suggestion that the two ends of the N-terminal inactivating peptide form a bivalent complex that simultaneously blocks the channel pore and binds to the cytoplasmic T1 domain, we propose a six state kinetic model that for the first time reproduces the kinetics of recovery of the Drosophila Shaker over the full range of time scales and hyperpolarization potentials, including tail currents. The model is motivated by a normal mode analysis of the inactivated channel that suggests that a displacement consistent with models of the closed state propagates to the T1 domain via the S1-T1 linker. This motion stretches the bound (inactivating) peptide, hastening the unblocking of the pore. This pulling force is incorporated into the rates of the open to blocked states, capturing the fast recovery phase of the current for repolarization events shorter than 1 ms. If the membrane potential is hyperpolarized, essential dynamics further suggests that the T1 domain returns to a configuration where the peptide is un-stretched and the S1-T1 linker is extended. Coupling this novel hyperpolarized substate to the closed, open and blocked pore states is enough to quantitatively estimate the number of open channels as a function of time and membrane potential. A straightforward prediction of the model is that a slow ramping of the potential leads to very small currents.

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Ball and spring bi-valent complex model of inactivating N-terminal peptide (red) and Shaker Kv1.2 [3].(A) Shaker includes the S1-T1 (G131-S159) domain modeled here, but has almost no bearing in the complex structure. For clarity, we removed the TM and linker domains of the cyan monomer, Y132-T421. The interaction [21] between the ball (M1-E9) and the pore is dominated by hydrophobic contacts involving residues I5, V3, C7 and M1, and the Valine ring in the pore V406, V410, and P407 (in yellow). On the other hand, the hydrophilic tail binds mostly due to Hydrogen bonds between peptide residues R15, R25, R20, R13 and L21, and T1 domain residues E136, E121, E56, D129, D107 (cyan monomer), E130, M125 and F126, respectively. Chemical affinity (electrostatic plus desolvation) of the ball and tail in the bound state is estimated to be −12 and −41 kcal/mol, respectively [21]. (B) Structural transition upon repolarization modeled using essential dynamics (see Methods). For clarity, only one of the four symmetric monomers is shown: Kv1.2 crystal structure (blue) as in Fig. 3A, repolarized (red) and hyperpolarized (green) models. Arrow indicates direction of S1 rotation due to repolarization. For comparison, inset shows the equivalent view of the S1 helix from the crystal and the “down” model of Yarov-Yarovoy et al. [16]. Also shown are the bound peptides (in yellow) for the crystal and hyperpolarized model structure.
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pone-0003342-g003: Ball and spring bi-valent complex model of inactivating N-terminal peptide (red) and Shaker Kv1.2 [3].(A) Shaker includes the S1-T1 (G131-S159) domain modeled here, but has almost no bearing in the complex structure. For clarity, we removed the TM and linker domains of the cyan monomer, Y132-T421. The interaction [21] between the ball (M1-E9) and the pore is dominated by hydrophobic contacts involving residues I5, V3, C7 and M1, and the Valine ring in the pore V406, V410, and P407 (in yellow). On the other hand, the hydrophilic tail binds mostly due to Hydrogen bonds between peptide residues R15, R25, R20, R13 and L21, and T1 domain residues E136, E121, E56, D129, D107 (cyan monomer), E130, M125 and F126, respectively. Chemical affinity (electrostatic plus desolvation) of the ball and tail in the bound state is estimated to be −12 and −41 kcal/mol, respectively [21]. (B) Structural transition upon repolarization modeled using essential dynamics (see Methods). For clarity, only one of the four symmetric monomers is shown: Kv1.2 crystal structure (blue) as in Fig. 3A, repolarized (red) and hyperpolarized (green) models. Arrow indicates direction of S1 rotation due to repolarization. For comparison, inset shows the equivalent view of the S1 helix from the crystal and the “down” model of Yarov-Yarovoy et al. [16]. Also shown are the bound peptides (in yellow) for the crystal and hyperpolarized model structure.

Mentions: The possibility of a relative displacement of the TM and T1 domain is further supported by a normal mode analysis applied to a structural model (as in Ref. [3]) of the blocked. We first note that both Yarov-Yarovoy et al. [16] and Grabe et al. [15] model of the down state translate in a counter-clock rotation of the outer TM helix S1. Using this rotation as a probe for the modes that might be sampled by voltage gating, we identified two modes (among the 30 slowest normal modes) that are consistent with the overall displacement of the S1 helix. In these two modes all four tetrameric domains move in synchrony and the outer S1 helix rotates counter-clockwise with respect to the pore (see inset in Fig. 3B for a comparison of the rotation of S1 between the open and closed state in [16] with respect to the one observed here). Mode 1 tilts S1, pushing the S1-T1 linker, which instead pushes T1 away from the TM domain (Fig. 4A). On the other hand, mode 2 pushes T1 sideways leading almost immediately to clashes, as the linker and T1 interface collapse with each other. A straightforward 4x30 steps energy minimization using CHARMm [26] confirms that the internal and van der Waals energies rapidly increase along mode 2, but not mode 1. Hence, the prediction is that repolarization triggers a structural rearrangement consistent with mode 1, which as shown in Fig. 4A pulls the bound peptide from the pore. This coupling between TM and T1 in the blocked state is consistent with an elastic force like the one modeled in Fig. 1C.


Quantitative modeling of currents from a voltage gated ion channel undergoing fast inactivation.

Camacho CJ - PLoS ONE (2008)

Ball and spring bi-valent complex model of inactivating N-terminal peptide (red) and Shaker Kv1.2 [3].(A) Shaker includes the S1-T1 (G131-S159) domain modeled here, but has almost no bearing in the complex structure. For clarity, we removed the TM and linker domains of the cyan monomer, Y132-T421. The interaction [21] between the ball (M1-E9) and the pore is dominated by hydrophobic contacts involving residues I5, V3, C7 and M1, and the Valine ring in the pore V406, V410, and P407 (in yellow). On the other hand, the hydrophilic tail binds mostly due to Hydrogen bonds between peptide residues R15, R25, R20, R13 and L21, and T1 domain residues E136, E121, E56, D129, D107 (cyan monomer), E130, M125 and F126, respectively. Chemical affinity (electrostatic plus desolvation) of the ball and tail in the bound state is estimated to be −12 and −41 kcal/mol, respectively [21]. (B) Structural transition upon repolarization modeled using essential dynamics (see Methods). For clarity, only one of the four symmetric monomers is shown: Kv1.2 crystal structure (blue) as in Fig. 3A, repolarized (red) and hyperpolarized (green) models. Arrow indicates direction of S1 rotation due to repolarization. For comparison, inset shows the equivalent view of the S1 helix from the crystal and the “down” model of Yarov-Yarovoy et al. [16]. Also shown are the bound peptides (in yellow) for the crystal and hyperpolarized model structure.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2551740&req=5

pone-0003342-g003: Ball and spring bi-valent complex model of inactivating N-terminal peptide (red) and Shaker Kv1.2 [3].(A) Shaker includes the S1-T1 (G131-S159) domain modeled here, but has almost no bearing in the complex structure. For clarity, we removed the TM and linker domains of the cyan monomer, Y132-T421. The interaction [21] between the ball (M1-E9) and the pore is dominated by hydrophobic contacts involving residues I5, V3, C7 and M1, and the Valine ring in the pore V406, V410, and P407 (in yellow). On the other hand, the hydrophilic tail binds mostly due to Hydrogen bonds between peptide residues R15, R25, R20, R13 and L21, and T1 domain residues E136, E121, E56, D129, D107 (cyan monomer), E130, M125 and F126, respectively. Chemical affinity (electrostatic plus desolvation) of the ball and tail in the bound state is estimated to be −12 and −41 kcal/mol, respectively [21]. (B) Structural transition upon repolarization modeled using essential dynamics (see Methods). For clarity, only one of the four symmetric monomers is shown: Kv1.2 crystal structure (blue) as in Fig. 3A, repolarized (red) and hyperpolarized (green) models. Arrow indicates direction of S1 rotation due to repolarization. For comparison, inset shows the equivalent view of the S1 helix from the crystal and the “down” model of Yarov-Yarovoy et al. [16]. Also shown are the bound peptides (in yellow) for the crystal and hyperpolarized model structure.
Mentions: The possibility of a relative displacement of the TM and T1 domain is further supported by a normal mode analysis applied to a structural model (as in Ref. [3]) of the blocked. We first note that both Yarov-Yarovoy et al. [16] and Grabe et al. [15] model of the down state translate in a counter-clock rotation of the outer TM helix S1. Using this rotation as a probe for the modes that might be sampled by voltage gating, we identified two modes (among the 30 slowest normal modes) that are consistent with the overall displacement of the S1 helix. In these two modes all four tetrameric domains move in synchrony and the outer S1 helix rotates counter-clockwise with respect to the pore (see inset in Fig. 3B for a comparison of the rotation of S1 between the open and closed state in [16] with respect to the one observed here). Mode 1 tilts S1, pushing the S1-T1 linker, which instead pushes T1 away from the TM domain (Fig. 4A). On the other hand, mode 2 pushes T1 sideways leading almost immediately to clashes, as the linker and T1 interface collapse with each other. A straightforward 4x30 steps energy minimization using CHARMm [26] confirms that the internal and van der Waals energies rapidly increase along mode 2, but not mode 1. Hence, the prediction is that repolarization triggers a structural rearrangement consistent with mode 1, which as shown in Fig. 4A pulls the bound peptide from the pore. This coupling between TM and T1 in the blocked state is consistent with an elastic force like the one modeled in Fig. 1C.

Bottom Line: If the membrane potential is hyperpolarized, essential dynamics further suggests that the T1 domain returns to a configuration where the peptide is un-stretched and the S1-T1 linker is extended.Coupling this novel hyperpolarized substate to the closed, open and blocked pore states is enough to quantitatively estimate the number of open channels as a function of time and membrane potential.A straightforward prediction of the model is that a slow ramping of the potential leads to very small currents.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. ccamacho@pitt.edu

ABSTRACT
Ion channels play a central role in setting gradients of ion concentration and electrostatic potentials, which in turn regulate sensory systems and other functions. Based on the structure of the open configuration of the Kv1.2 channel and the suggestion that the two ends of the N-terminal inactivating peptide form a bivalent complex that simultaneously blocks the channel pore and binds to the cytoplasmic T1 domain, we propose a six state kinetic model that for the first time reproduces the kinetics of recovery of the Drosophila Shaker over the full range of time scales and hyperpolarization potentials, including tail currents. The model is motivated by a normal mode analysis of the inactivated channel that suggests that a displacement consistent with models of the closed state propagates to the T1 domain via the S1-T1 linker. This motion stretches the bound (inactivating) peptide, hastening the unblocking of the pore. This pulling force is incorporated into the rates of the open to blocked states, capturing the fast recovery phase of the current for repolarization events shorter than 1 ms. If the membrane potential is hyperpolarized, essential dynamics further suggests that the T1 domain returns to a configuration where the peptide is un-stretched and the S1-T1 linker is extended. Coupling this novel hyperpolarized substate to the closed, open and blocked pore states is enough to quantitatively estimate the number of open channels as a function of time and membrane potential. A straightforward prediction of the model is that a slow ramping of the potential leads to very small currents.

Show MeSH
Related in: MedlinePlus