Energetic Determinants of Oligomeric State Specificity in Coiled Coils[J. Am. Chem. Soc. 2006, 128, 1549915510]. Jorge Ramos and Themis Lazaridis* Pages 15503, 15505, 15506, and 15507 respectively: Tables Table 2. Average Free Energy (W - T∆Sconf) per Residue for the GCN4-p1 Sequence during Four 0.6 ns (300 Frames) Nose´ -Hoover MD Simulationsa residue
I
II
III
IV
V
Ace Arg2g Met3a Lys4b Gln5c Leu6d Glu7e Asp8f Lys9g Val10a Glu11b Glu12c Leu13d Leu14e Ser15f Lys16g Asn17a Tyr18b His19c Leu20d Glu21e Asn22f Glu23g Val24a Ala25b b Arg26c Leu27d Lys28e Lys29f Leu30g Val31a Cbx ∑[W - T∆Sconf]
-4.04 4.04 -1.97 0.86 -8.50 -4.21 -3.49 -10.47 -1.17 -2.53 -4.15 -4.45 -4.68 -5.78 -8.21 0.14 -11.57 -1.42 -3.32 -4.52 -4.19 -11.63 -3.97 -2.61 -5.51 1.24 -4.03 1.30 1.75 -1.78 2.20 -1.41 -108.08
-3.31 3.39 -1.62 1.26 -8.61 -6.92 -4.53 -10.84 -0.99 -4.63 -4.79 -4.86 -7.70 -5.81 -7.96 0.71 -11.19 -1.57 -3.28 -6.60 -4.63 -11.35 -3.74 -3.68 -6.39 1.87 -6.81 0.59 1.61 -1.70 2.17 -1.39 -123.32
-4.58 6.29 -1.18 1.05 -8.49 -5.90 -4.12 -10.64 -0.66 -4.82 -4.45 -4.44 -6.08 -5.86 -7.81 1.52 -12.22 -1.18 -3.41 -6.31 -4.36 -11.49 -4.16 -4.46 -6.21 1.96 -6.45 1.10 1.85 -1.70 1.08 -1.44 -117.58
-4.60 6.93 -0.75 0.88 -8.28 -5.49 -3.66 -10.33 -0.56 -4.30 -3.97 -4.06 -6.78 -6.45 -8.41 1.04 -10.81 -0.51 -3.70 -6.49 -4.60 -11.14 -4.04 -3.87 -5.93 1.76 -6.35 1.33 1.65 -2.40 1.32 -1.62 -114.15
-4.58 5.34 -1.94 0.88 -8.27 -6.00 -4.67 -10.82 -0.34 -4.47 -4.43 -4.40 -7.18 -5.40 -7.98 1.51 -10.68 -0.83 -4.14 -5.92 -3.68 -11.12 -3.99 -4.40 -6.14 2.14 -6.70 1.33 2.71 -2.86 0.31 -1.97 -118.69
a All entries are in units of kcal/(mol‚helix). Lowest energy values among the oligomers are underlined. The monomer energies have been included for completeness, but only the multimers are compared. The values reported here do not include the constant ∑i∆Girefsolv contribution. The error bar on these values is around 0.1 kcal/mol. Ace is the acetyl blocking group, and Cbx, the methyl amide blocking group. b The stabilization observed for Ala25b is an artifact, resulting from the rebuilding of part of helix A of the trimer (see Methods). This rebuilding results in a suboptimal hydrogen bond between Ala25b and Lys.29f
10.1021/ja076882k CCC: $37.00 © 2007 American Chemical Society
2, 3, 4, and 5 contain an error (column V is identical to column I). The corrected tables are provided below. The text is not affected by this error. We thank David Minde for pointing out the error. Table 3. Average Free Energy (W - T∆Sconf) per Residue for the H38-p1 Sequence during Four 0.6 ns (300 Frames) Nose´ -Hoover MD Simulationsa residue
I
II
III
IV
V
Ace Arg2g Ile3a Lys4b Gln5c Gln6d Glu7e Asp8f Lys9g Leu10a Glu11b Glu12c Thr13d Leu14e Ser15f Lys16g Ile17a Tyr18b His19c Leu20d Glu21e Asn22f Glu23g Ile24a Ala25b Arg26c Val27d Lys28e Lys29f Leu30g Leu31a Cbx ∑[W - T∆Sconf]
-4.67 3.79 -0.20 0.58 -8.16 -9.33 -4.03 -10.62 -2.35 -4.30 -4.81 -4.95 -4.85 -5.24 -8.11 0.03 -3.11 -1.30 -3.51 -4.76 -3.56 -11.28 -4.10 -1.89 -5.61 1.22 -2.71 1.36 1.96 -1.92 1.21 -1.39 -106.62
-3.46 2.10 -0.98 1.35 -8.20 -10.37 -3.95 -10.87 -1.22 -4.22 -4.92 -5.47 -5.16 -5.24 -7.75 0.64 -3.12 -1.19 -3.67 -7.36 -3.26 -11.43 -3.79 -1.57 -6.16 1.95 -3.45 0.73 1.94 -1.94 1.94 -1.26 -109.35
-4.91 3.71 -1.32 0.80 -8.43 -10.86 -4.10 -10.63 -2.45 -6.24 -4.74 -5.13 -5.35 -5.53 -7.78 1.18 -4.66 -1.21 -3.45 -6.93 -3.49 -11.40 -4.29 -3.77 -6.13 1.17 -4.74 1.07 1.88 -2.05 -0.03 -1.56 -121.36
-4.80 3.79 -0.07 1.03 -7.78 -10.84 -3.79 -10.44 -2.45 -6.28 -4.21 -4.83 -5.65 -5.05 -8.13 1.23 -4.02 -0.23 -3.68 -7.08 -4.18 -11.15 -5.01 -3.22 -6.01 1.22 -4.64 1.31 1.84 -3.15 -1.24 -1.66 -119.17
-4.65 3.72 -0.79 0.90 -8.41 -10.45 -4.43 -10.87 -1.69 -6.21 -4.90 -4.98 -5.32 -4.00 -8.09 1.22 -3.71 -0.71 -4.05 -6.53 -2.97 -10.87 -4.09 -3.46 -6.09 1.40 -4.27 1.59 2.00 -3.09 -1.41 -1.91 -117.13
a All entries are in units of kcal/(mol‚helix). Lowest energy values among the oligomers are underlined. The monomer energies have been included for completeness, but only the multimers are compared. The values reported here do not include the constant ∑i∆Girefsolv contribution. The error bar on these values is around 0.1 kcal/mol. Ace is the acetyl blocking group, and Cbx, the methyl amide blocking group.
J. AM. CHEM. SOC. 2007, 129, 3455-3456
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ADDITIONS AND CORRECTIONS Table 4. Average Free Energy (W - T∆Sconf) per Residue for the Gcn4-LI Sequence during Four 0.6 ns (300 Frames) Nose´ -Hoover MD Simulationsa
Table 5. Average Free Energy (W - T∆Sconf) per Residue for the Comp Sequence during Four 0.6 ns (300 Frames) Nose´ -Hoover MD Simulationsa
residue
I
II
III
IV
V
residue
I
II
III
IV
V
Ace Arg2g Met3a Lys4b Gln5c Ile6d Glu7e Asp8f Lys9g Leu10a Glu11b Glu12c Ile13d Leu14e Ser15f Lys16g Leu17a Tyr18b His19c Ile20d Glu21e Asn22f Glu23g Leu24a Ala25b Arg26c Ile27d Lys28e Lys29f Leu30g Leu31a Cbx ∑[W - T∆Sconf]
-4.78 5.27 -2.12 0.02 -9.21 -1.68 -4.07 -10.19 -1.40 -4.17 -4.73 -4.32 -2.21 -5.72 -8.06 -0.14 -5.56 -1.36 -3.53 -2.40 -3.38 -11.30 -3.82 -4.15 -5.71 0.89 -1.61 1.60 1.80 -2.09 0.77 -1.35 -98.70
-3.39 4.10 -1.23 1.55 -8.75 -3.20 -4.10 -10.72 -1.41 -4.87 -4.70 -4.76 -3.04 -6.05 -7.93 -0.32 -6.49 -1.44 -3.47 -2.52 -3.78 -11.56 -3.85 -4.63 -6.29 1.41 -2.54 0.86 2.06 -2.06 2.04 -1.20 -102.28
-4.45 5.85 -0.54 0.78 -8.43 -3.91 -4.06 -10.52 -0.50 -5.71 -5.01 -4.53 -4.39 -6.14 -7.73 1.38 -7.09 -1.33 -3.35 -4.23 -3.56 -11.51 -3.90 -5.74 -6.31 1.63 -4.22 0.65 1.33 -1.96 -0.14 -1.58 -109.22
-4.56 6.49 -1.22 0.50 -8.31 -3.92 -3.72 -10.14 -0.86 -7.18 -4.55 -4.18 -4.97 -6.53 -7.95 0.66 -7.71 -0.60 -3.78 -4.95 -4.21 -11.08 -4.67 -7.31 -6.23 1.23 -4.21 1.01 1.82 -3.09 -1.60 -1.68 -117.52
-4.30 6.11 -1.65 0.89 -8.46 -3.66 -4.20 -10.38 -0.24 -7.33 -4.96 -4.45 -4.41 -5.50 -7.93 0.43 -7.56 -1.01 -4.47 -4.62 -3.41 -10.87 -3.87 -7.73 -6.39 1.74 -4.22 1.13 1.86 -3.17 -1.56 -1.94 -116.15
Ace Leu2g Ala3a Pro4b Gln5c Met6d Leu7e Arg8f Glu9g Leu10a Gln11b Glu12c Thr13d Asn14e Ala15f Ala16g Leu17a Gln18b Asp19c Val20d Arg21e Glu22f Leu23g Leu24a Arg25b Gln26c Gln27d Val28e Lys29f Glu30g Ile31a Cbx ∑[W - T∆Sconf]
-3.16 -3.27 0.09 5.56 -8.04 -4.51 -5.05 1.46 -5.91 -4.57 -8.65 -5.20 -4.57 -10.59 -6.72 -6.56 -4.15 -8.99 -10.33 -3.07 2.48 -4.44 -4.95 -4.40 2.95 -9.63 -8.00 -1.49 1.85 -1.38 3.57 -1.48 -121.15
-3.33 -2.92 -0.41 5.48 -8.38 -3.87 -4.76 1.55 -6.04 -4.92 -8.44 -5.42 -4.39 -10.99 -6.81 -7.12 -4.78 -9.20 -10.17 -4.01 2.36 -4.24 -5.27 -5.37 2.23 -8.74 -7.63 -2.27 1.90 -1.78 3.53 -1.29 -125.51
-3.75 -2.71 -0.48 5.25 -8.46 -4.33 -5.23 1.44 -6.36 -6.29 -8.60 -5.52 -6.06 -11.43 -6.68 -7.20 -5.09 -9.16 -10.63 -4.35 3.30 -4.44 -5.20 -6.46 2.44 -9.50 -9.67 -2.09 1.89 -1.60 2.45 -1.48 -135.98
-3.68 -2.42 0.14 4.84 -8.46 -4.09 -5.07 2.21 -6.28 -6.71 -8.49 -4.94 -5.23 -10.56 -6.64 -7.42 -5.55 -8.50 -10.45 -5.27 2.54 -4.20 -6.27 -6.86 3.62 -10.01 -9.31 -2.98 1.31 -1.77 2.16 -1.58 -135.94
-3.71 -2.74 -0.93 4.98 -8.65 -4.57 -5.23 1.84 -5.65 -6.76 -8.94 -5.43 -5.34 -11.26 -6.18 -7.92 -5.64 -8.95 -9.65 -4.92 1.73 -4.31 -7.06 -6.88 3.00 -9.25 -10.24 -4.01 2.40 -0.95 1.69 -2.03 -141.56
a All entries are in units of kcal/(mol‚helix). Lowest energy values among the oligomers are underlined. The monomer energies have been included for completeness, but only the multimers are compared. The values reported here do not include the constant ∑i∆Girefsolv contribution. The error bar on these values is around 0.1 kcal/mol. Ace is the acetyl blocking group, and Cbx, the methyl amide blocking group.
JA076882K 10.1021/ja076882k Published on Web 02/27/2007
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VOL. 129, NO. 11, 2007
a All entries are in units of kcal/(mol‚helix). Lowest energy values among the oligomers are underlined. The monomer energies have been included for completeness, but only the multimers are compared. The values reported here do not include the constant ∑i∆Girefsolv contribution. The error bar on these values is around 0.1 kcal/mol. Ace is the acetyl blocking group, and Cbx, the methyl amide blocking group.
