Volume 12, Issue 12, Pages 2221-2231 (December 2004) Phage Like It HOT  Eugene F. DeRose, Thomas W. Kirby, Geoffrey A. Mueller, Anna K. Chikova, Roel M. Schaaper, Robert E. London  Structure  Volume 12, Issue 12, Pages 2221-2231 (December 2004) DOI: 10.1016/j.str.2004.09.019

Figure 1 CLUSTAL W Alignment of θ and HOT, Showing 53% Sequence Identity Identical residues are shown in red. α-helical residues in HOT, as indicated by TALOS analysis, and in θ, based on Keniry et al. (2000), are underlined. Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 2 1H-15N HSQC Spectrum of U-[13C,15N]HOT The spectrum was obtained by using Varian's gNhsqc sequence on a UNITYINOVA 600 MHz spectrometer, with 128 × 512 complex points and acquisition times of 71 and 64 ms in t1 and t2, respectively. Eight scans were acquired per increment, with a 1.0 s delay between scans. The protein was in 5 mM Tris-d11 (pH 7.0) buffer and 100 mM NaCl. All spectra were obtained at 25°C. Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 3 Global Fold of HOT (A) Ribbon rendering (residues 11–66) of the average solution structure of HOT computed from the seven lowest-energy structures obtained by using RDC restraints and starting from a random extended structure. The locations of the three α helices, α1, α2, and α3, as well as the two connecting loops, L1 and L2, are shown. (B) Backbone overlay (residues 11–66) of the seven lowest-energy structures of HOT, exhibiting an average rmsd with respect to the mean structure of 0.52 ± 0.10 Å. The α helices are rendered in red. All figures of HOT were generated with MOLMOL (Koradi et al., 1996). Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 4 Side Chain Heavy Atom Positions in the α Helices of HOT (A) Ribbon rendering (residues 11–66) of the lowest-energy structure of HOT showing the side chain heavy atoms of all residues in α helices 1–3. (B) Ribbon rendering rotated 180° about a vertical axis in the page, with respect to the view in (A). Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 5 Comparison of HOT and θ (1DU2) Structures (A and B) Comparison of (A) the lowest-energy HOT structure and (B) the best θ structure (1DU2, model 1, Keniry et al., 2000), showing that the two structures exhibit completely different folds. A ribbon rendering (residues 11–66) of both structures is shown. The structures superimpose with a backbone rmsd (residues 11–66) of 8.61 Å. Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 6 Comparison of Measured and Calculated Residual Dipolar Couplings for θ (A and B) Comparison of measured RDC constants with values (A) calculated by using model 1 from the ensemble published as 1DU2 (Keniry et al. 2000) or (B) calculated from a HOT-based homology model of θ. The data correspond to 30 amide resonances that were unambiguously assigned based on a comparison of our HSQC spectrum with that reported by Keniry et al. (2000). (A) corresponds to a correlation coefficient of 0.036, while (B) yields a correlation coefficient of 0.795. Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 7 Circular Dichroism Spectra of HOT and θ as a Function of Temperature The ellipticity at 220 nm was monitored for both HOT (circle) and θ square) over the range of 26°C–80°C. Protein concentration was 2.1 μM in 10 mM NaPi buffer (pH 6.5). The smooth curves correspond to the best fits of Equation 1 to the data. From the data fits, the melting temperatures for HOT and θ were determined as 62.1°C and 56.0°C, respectively. Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)

Figure 8 Electrostatic Surface of HOT (A) Electrostatic surface rendering (residues 11–66) of the lowest-energy structure of HOT, showing hydrophobic residues that may be involved in binding to ϵ. Red intensity is proportional to local negative charge, blue intensity is proportional to local positive charge, and white corresponds to uncharged regions of the protein surface. (B) View of the electrostatic surface, rotated 180° about a vertical axis through the page relative to the orientation shown in (A). Structure 2004 12, 2221-2231DOI: (10.1016/j.str.2004.09.019)