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alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

Li-Smerin Y, Hackos DH, Swartz KJ - J. Gen. Physiol. (2000)

Bottom Line: Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure.The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments.In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

View Article: PubMed Central - PubMed

Affiliation: Molecular Physiology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA.

ABSTRACT
Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

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Periodicity of gating perturbations in the S3–S4 linker. (A) Amino acid sequence of the S3–S4 linker in the drk1 K+ channel. The bar indicates the stretch used for Fourier transform analysis. (B) The power spectrum of the /ΔΔG0/ values for this stretch, where P(ω) is plotted as a function of angular frequency (ω). The primary peak of power spectrum occurs at 104°. (C) Helical wheel diagram of these 17 residues viewed from the NH2 terminus. Large shaded circles indicate positions with /ΔΔG0/ > 0.5 kcal mol−1 and large open circles indicate positions with /ΔΔG0/ ≤ 0.5 kcal mol−1.
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Figure 11: Periodicity of gating perturbations in the S3–S4 linker. (A) Amino acid sequence of the S3–S4 linker in the drk1 K+ channel. The bar indicates the stretch used for Fourier transform analysis. (B) The power spectrum of the /ΔΔG0/ values for this stretch, where P(ω) is plotted as a function of angular frequency (ω). The primary peak of power spectrum occurs at 104°. (C) Helical wheel diagram of these 17 residues viewed from the NH2 terminus. Large shaded circles indicate positions with /ΔΔG0/ > 0.5 kcal mol−1 and large open circles indicate positions with /ΔΔG0/ ≤ 0.5 kcal mol−1.

Mentions: Fig. 9 shows a sliding window analysis of α-PI beginning at the NH2 terminus of S1 and ending at the COOH terminus of S4. A 13-residue window is shown in A and a 17-residue window is shown in B. A sliding window hydrophobicity analysis is also shown for comparison. The comparison between the α-PI and the hydrophobicity index is quite remarkable for two reasons. First, there is an excellent correlation between the α-PI and hydrophobicity index for all four transmembrane segments, especially for S1, S2, and S3. For the 13-residue window, α-PI values greater than 2 are observed for S1, S2, and S3 and a value of 1.9 is seen for S4. This high degree of correspondence between α-PI and hydrophobicity makes it highly probable that all four transmembrane segments are in fact α-helical in structure. A second remarkable aspect of the graph is that within the two extracellular linkers (S1–S2 and S3–S4) there are peaks in the α-PI that correspond to troughs in the hydrophobicity index. For the 17-residue window, peak α-PI values of 2.1 and 1.6 are observed for the S1–S2 and S3–S4 linkers, respectively. In contrast, for the S2–S3 linker, a corresponding minimum is observed for both the α-PI and hydrophobicity index. Fig. 10 and Fig. 11 show power spectra and helical wheel diagrams for the S1–S2 and S3–S4 linkers, respectively. Both spectra show dominant peaks within the α-helical frequency range and both helical wheels show clustering of residues with small versus moderate effects on gating. These results raise the possibility that there is an additional α-helix in each of the two extracellular linkers.


alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

Li-Smerin Y, Hackos DH, Swartz KJ - J. Gen. Physiol. (2000)

Periodicity of gating perturbations in the S3–S4 linker. (A) Amino acid sequence of the S3–S4 linker in the drk1 K+ channel. The bar indicates the stretch used for Fourier transform analysis. (B) The power spectrum of the /ΔΔG0/ values for this stretch, where P(ω) is plotted as a function of angular frequency (ω). The primary peak of power spectrum occurs at 104°. (C) Helical wheel diagram of these 17 residues viewed from the NH2 terminus. Large shaded circles indicate positions with /ΔΔG0/ > 0.5 kcal mol−1 and large open circles indicate positions with /ΔΔG0/ ≤ 0.5 kcal mol−1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1887781&req=5

Figure 11: Periodicity of gating perturbations in the S3–S4 linker. (A) Amino acid sequence of the S3–S4 linker in the drk1 K+ channel. The bar indicates the stretch used for Fourier transform analysis. (B) The power spectrum of the /ΔΔG0/ values for this stretch, where P(ω) is plotted as a function of angular frequency (ω). The primary peak of power spectrum occurs at 104°. (C) Helical wheel diagram of these 17 residues viewed from the NH2 terminus. Large shaded circles indicate positions with /ΔΔG0/ > 0.5 kcal mol−1 and large open circles indicate positions with /ΔΔG0/ ≤ 0.5 kcal mol−1.
Mentions: Fig. 9 shows a sliding window analysis of α-PI beginning at the NH2 terminus of S1 and ending at the COOH terminus of S4. A 13-residue window is shown in A and a 17-residue window is shown in B. A sliding window hydrophobicity analysis is also shown for comparison. The comparison between the α-PI and the hydrophobicity index is quite remarkable for two reasons. First, there is an excellent correlation between the α-PI and hydrophobicity index for all four transmembrane segments, especially for S1, S2, and S3. For the 13-residue window, α-PI values greater than 2 are observed for S1, S2, and S3 and a value of 1.9 is seen for S4. This high degree of correspondence between α-PI and hydrophobicity makes it highly probable that all four transmembrane segments are in fact α-helical in structure. A second remarkable aspect of the graph is that within the two extracellular linkers (S1–S2 and S3–S4) there are peaks in the α-PI that correspond to troughs in the hydrophobicity index. For the 17-residue window, peak α-PI values of 2.1 and 1.6 are observed for the S1–S2 and S3–S4 linkers, respectively. In contrast, for the S2–S3 linker, a corresponding minimum is observed for both the α-PI and hydrophobicity index. Fig. 10 and Fig. 11 show power spectra and helical wheel diagrams for the S1–S2 and S3–S4 linkers, respectively. Both spectra show dominant peaks within the α-helical frequency range and both helical wheels show clustering of residues with small versus moderate effects on gating. These results raise the possibility that there is an additional α-helix in each of the two extracellular linkers.

Bottom Line: Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure.The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments.In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

View Article: PubMed Central - PubMed

Affiliation: Molecular Physiology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA.

ABSTRACT
Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

Show MeSH
Related in: MedlinePlus