BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 3 7 4 315.93 3.62 2 3 86 83 37.33 0.39 3 4 7 3 318.23 2.47 4 4 8 4 312.77 3.63 5 4 17 13 70.42 2.17 6 4 20 16 69.62 2.22 7 4 21 17 69.64 2.21 8 5 8 3 323.05 1.51 9 5 9 4 313.22 3.41 10 6 9 3 320.64 1.11 11 6 10 4 313.21 3.41 12 6 82 76 46.27 1.04 13 6 85 79 45.91 0.91 14 6 86 80 45.71 0.90 15 6 89 83 43.32 0.62 16 7 10 3 319.23 0.41 17 7 11 4 304.16 0.77 18 7 15 8 75.14 2.51 19 7 20 13 73.30 2.46 20 7 23 16 72.81 2.21 21 7 24 17 71.52 2.85 22 7 78 71 48.05 1.31 23 7 79 72 47.91 1.35 24 7 82 75 46.23 1.06 25 8 11 3 308.07 2.42 26 8 12 4 301.87 0.37 27 8 13 5 274.92 5.84 28 8 15 7 74.69 2.29 29 8 16 8 74.77 2.31 30 8 17 9 74.77 2.31 31 8 20 12 73.88 2.18 32 9 12 3 318.27 0.78 33 9 85 76 46.77 1.16 34 10 78 68 48.45 1.13 35 10 81 71 47.81 1.31 36 10 82 72 47.67 1.27 37 11 14 3 322.91 1.43 38 11 15 4 289.45 1.92 39 11 78 67 48.65 1.02 40 14 59 45 87.45 3.08 41 15 19 4 302.94 0.14 42 15 20 5 302.73 0.21 43 15 23 8 289.90 4.30 44 15 56 41 101.07 3.70 45 15 61 46 101.06 3.70 46 16 19 3 324.62 0.55 47 16 20 4 307.13 2.23 48 17 20 3 316.94 0.94 49 17 21 4 311.56 0.02 50 18 21 3 317.12 0.51 51 18 22 4 315.29 0.41 52 18 44 26 167.13 0.81 53 18 48 30 166.87 0.89 54 19 22 3 317.12 0.51 55 19 23 4 314.10 0.20 56 19 56 37 162.57 0.36 57 20 23 3 314.80 0.53 58 20 24 4 314.93 0.59 59 21 24 3 323.04 3.46 60 21 25 4 314.93 0.59 61 21 41 20 170.49 0.12 62 21 44 23 170.48 0.13 63 22 25 3 318.72 2.49 64 22 26 4 314.92 0.60 65 22 37 15 170.32 0.07 66 22 41 19 170.55 0.14 67 22 49 27 169.22 0.19 68 22 52 30 167.02 0.89 69 22 53 31 166.97 0.92 70 22 56 34 166.80 0.83 71 23 26 3 321.46 2.67 72 23 27 4 314.12 0.22 73 23 56 33 166.90 0.89 74 23 61 38 166.64 0.77 75 23 62 39 166.64 0.76 76 23 71 48 166.49 0.77 77 23 75 52 123.59 3.35 78 23 78 55 81.67 0.42 79 23 79 56 62.44 7.88 80 24 27 3 314.21 0.27 81 24 28 4 314.11 0.23 82 24 79 55 79.50 0.64 83 25 28 3 324.83 0.98 84 25 29 4 311.89 2.02 85 25 32 7 217.46 2.06 86 25 37 12 170.33 0.07 87 25 40 15 170.69 0.11 88 25 41 16 170.72 0.11 89 26 29 3 320.13 1.36 90 26 32 6 180.55 4.83 91 26 37 11 170.54 0.14 92 26 62 36 166.89 0.88 93 26 69 43 166.78 0.82 94 26 70 44 166.76 0.82 95 26 71 45 166.59 0.80 96 27 71 44 166.52 0.77 97 27 79 52 81.86 0.35 98 29 32 3 317.89 2.48 99 29 36 7 279.92 3.32 100 30 70 40 170.02 0.20 101 31 68 37 170.47 0.15 102 31 69 38 170.16 0.14 103 31 70 39 170.13 0.15 104 32 36 4 315.38 0.32 105 32 37 5 309.95 1.24 106 32 68 36 170.66 0.15 107 32 69 37 170.58 0.16 108 33 36 3 319.05 2.16 109 33 37 4 315.37 0.32 110 33 67 34 170.68 0.15 111 33 68 35 170.66 0.14 112 33 69 36 170.67 0.15 113 34 37 3 316.24 0.10 114 34 38 4 315.36 0.34 115 34 53 19 170.72 0.15 116 34 69 35 170.69 0.14 117 35 38 3 317.61 0.36 118 35 39 4 317.18 0.58 119 36 39 3 311.06 1.50 120 36 40 4 310.25 1.10 121 37 40 3 331.35 1.28 122 37 41 4 309.38 0.65 123 37 49 12 171.03 0.19 124 37 53 16 170.96 0.18 125 37 69 32 170.67 0.14 126 38 41 3 321.73 0.71 127 38 46 8 171.05 0.18 128 38 49 11 171.03 0.19 129 38 50 12 171.03 0.19 130 39 42 3 322.49 1.08 131 41 44 3 324.78 2.39 132 41 49 8 199.78 1.93 133 44 48 4 309.45 0.69 134 44 49 5 294.44 1.94 135 45 48 3 311.14 1.53 136 45 49 4 309.70 0.73 137 46 49 3 315.45 0.29 138 46 50 4 309.70 0.72 139 47 50 3 312.29 2.01 140 47 51 4 309.69 0.72 141 48 51 3 314.10 1.10 142 48 52 4 309.69 0.72 143 49 52 3 318.05 0.88 144 49 53 4 306.44 1.40 145 50 53 3 314.61 2.67 146 50 54 4 309.24 0.01 147 51 54 3 315.31 2.32 148 51 55 4 312.63 3.68 149 52 55 3 320.22 0.12 150 52 56 4 315.35 2.32 151 53 56 3 317.68 3.48 152 53 57 4 315.35 2.32 153 53 69 16 183.01 2.25 154 54 57 3 318.19 0.90 155 54 58 4 306.87 1.84 156 55 58 3 316.86 3.06 157 55 59 4 311.65 0.55 158 56 59 3 320.75 1.11 159 56 60 4 309.38 1.69 160 56 61 5 282.59 3.32 161 56 62 6 219.06 2.21 162 57 60 3 320.75 1.11 163 57 62 5 249.71 13.10 164 57 63 6 219.06 2.22 165 57 64 7 219.06 2.22 166 57 69 12 183.49 2.10 167 60 72 12 183.00 2.25 168 60 74 14 182.90 2.29 169 61 71 10 183.11 2.21 170 61 72 11 183.00 2.25 171 61 74 13 182.91 2.29 172 61 75 14 182.68 2.35 173 61 78 17 182.85 2.27 174 62 69 7 183.49 2.10 175 62 70 8 183.19 2.21 176 62 71 9 183.02 2.26 177 62 72 10 183.00 2.25 178 63 69 6 183.50 2.10 179 63 70 7 183.34 2.14 180 63 72 9 183.12 2.21 181 64 68 4 222.53 17.41 182 64 69 5 183.50 2.10 183 65 68 3 313.60 1.51 184 71 75 4 308.69 2.29 185 71 76 5 304.61 0.40 186 72 75 3 316.49 1.35 187 72 76 4 311.48 0.92 188 73 76 3 313.01 0.39 189 73 77 4 310.59 3.00 190 74 77 3 319.33 1.37 191 74 78 4 319.33 1.37 192 75 78 3 320.20 0.94 193 75 79 4 319.32 1.38 194 76 79 3 315.25 3.41 195 76 80 4 306.63 0.89 196 77 80 3 316.75 1.33 197 77 81 4 306.63 0.90 198 78 81 3 326.35 2.50 199 78 82 4 306.90 1.02 200 79 82 3 321.50 0.08 201 79 83 4 309.99 0.34 202 80 83 3 317.88 1.73 203 80 84 4 317.70 1.81 204 81 84 3 321.06 0.67 205 81 85 4 311.69 1.19 206 82 85 3 320.22 0.24 207 82 86 4 311.26 0.97 208 83 86 3 322.69 0.99 209 83 87 4 309.86 0.52 210 84 87 3 320.69 0.01 211 84 88 4 320.68 0.01 212 85 88 3 324.53 1.67 213 85 89 4 315.78 2.44 214 86 89 3 319.98 0.34 215 86 90 4 306.04 0.52 216 86 94 8 253.38 0.94 217 87 90 3 325.11 1.63 218 87 91 4 293.36 4.14 219 87 94 7 253.34 0.96 220 88 91 3 316.70 0.52 221 90 93 3 311.18 1.24 222 90 94 4 302.88 3.81 223 91 94 3 318.93 1.31 224 91 95 4 302.87 3.81 225 92 96 4 310.95 2.33 226 93 96 3 337.69 2.62