Figure 9.
Figure 9. Analysis of results for the TH6–TH7 segment. (A) Plot of the relative accessibility value, f, against residue number for the T-domain TH6–TH7 segment. Based on macroscopic experiments using MTS-ET (▼, ▽) or single-channel experiments using MTS-glucose (●, ○), f was calculated from Eq. 3. Closed symbols are used for residues that were observed to react primarily in the open state, as well as for those that showed protection from reaction by His6-tag blocking; open symbols are used for the other residues. (Data for G315C are included, despite its abnormally high single-channel conductance.) Note that in the MTS-ET experiments (except with A302C, S305C, I306C, and S312C), the rates were measured at positive voltage, which may exaggerate the proximity of the mutated residues to the cis side. This panel is based on data in Tables 1, 2, and 4. Using a Taylor series approximation for the function f(x, y) = 1/(1 + x/y), we estimated its mean as μf ≈ 1/(1 + μx/μy), and its SD as σf ≈ (μy2σx2 + μx2σy2)1/2/(μx + μy)2. For macroscopic data, μ is the mean of k, σ is the SD of k, and the x and y subscripts refer to cis and trans, respectively. For single-channel data, μ = τ (the mean waiting time), σ = τ/n1/2 (an estimate of the SD of τ, based on the assumption of exponentially distributed waiting times), and the x and y subscripts refer to trans and cis, respectively. The error bars represent the SD of f. Error bars smaller than the symbols were omitted. (B) Mapping of the relative accessibility values, f, for the TH6–TH7 segment onto the aqueous crystal structure of DT. The segment from residues 297–317 is shown. Residues represented by closed symbols in A are colored red, orange, yellow, or green to represent f values of ∼0.0, 0.2–0.3, 0.6–0.8, or 1.0, respectively. There is a rough correlation between f and the vertical position in the figure. Residues 297–317 were excerpted from the crystal structure of whole DT (Bennett et al., 1994), available from the Protein Data Bank (Berman et al., 2000) under accession no. 1DDT, and displayed using PyMOL (1.7.2.1). The polypeptide backbone is represented as a ribbon in α-helical regions and as a narrow tube in loop regions. Side chains are shown as stick figures.

Analysis of results for the TH6–TH7 segment. (A) Plot of the relative accessibility value, f, against residue number for the T-domain TH6–TH7 segment. Based on macroscopic experiments using MTS-ET (▼, ▽) or single-channel experiments using MTS-glucose (●, ○), f was calculated from Eq. 3. Closed symbols are used for residues that were observed to react primarily in the open state, as well as for those that showed protection from reaction by His6-tag blocking; open symbols are used for the other residues. (Data for G315C are included, despite its abnormally high single-channel conductance.) Note that in the MTS-ET experiments (except with A302C, S305C, I306C, and S312C), the rates were measured at positive voltage, which may exaggerate the proximity of the mutated residues to the cis side. This panel is based on data in Tables 1, 2, and 4. Using a Taylor series approximation for the function f(x, y) = 1/(1 + x/y), we estimated its mean as μf ≈ 1/(1 + μx/μy), and its SD as σf ≈ (μy2σx2 + μx2σy2)1/2/(μx + μy)2. For macroscopic data, μ is the mean of k, σ is the SD of k, and the x and y subscripts refer to cis and trans, respectively. For single-channel data, μ = τ (the mean waiting time), σ = τ/n1/2 (an estimate of the SD of τ, based on the assumption of exponentially distributed waiting times), and the x and y subscripts refer to trans and cis, respectively. The error bars represent the SD of f. Error bars smaller than the symbols were omitted. (B) Mapping of the relative accessibility values, f, for the TH6–TH7 segment onto the aqueous crystal structure of DT. The segment from residues 297–317 is shown. Residues represented by closed symbols in A are colored red, orange, yellow, or green to represent f values of ∼0.0, 0.2–0.3, 0.6–0.8, or 1.0, respectively. There is a rough correlation between f and the vertical position in the figure. Residues 297–317 were excerpted from the crystal structure of whole DT (Bennett et al., 1994), available from the Protein Data Bank (Berman et al., 2000) under accession no. 1DDT, and displayed using PyMOL (1.7.2.1). The polypeptide backbone is represented as a ribbon in α-helical regions and as a narrow tube in loop regions. Side chains are shown as stick figures.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal