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 8 11 3 454.84 5.50 2 8 12 4 431.36 3.12 3 8 52 44 295.52 0.33 4 9 12 3 459.94 2.89 5 9 13 4 449.43 4.83 6 9 46 37 295.93 0.54 7 9 50 41 296.91 0.42 8 9 52 43 295.53 0.34 9 9 53 44 295.76 0.45 10 9 54 45 295.48 0.35 11 9 62 53 292.09 0.53 12 10 13 3 457.36 3.73 13 10 14 4 449.92 5.07 14 10 46 36 295.92 0.53 15 10 48 38 296.99 0.42 16 10 49 39 296.95 0.41 17 10 50 40 296.94 0.42 18 11 15 4 452.96 6.58 19 12 15 3 458.29 3.92 20 12 16 4 458.13 4.00 21 12 42 30 296.62 0.20 22 12 62 50 295.50 0.35 23 12 66 54 294.97 0.24 24 13 16 3 468.06 3.75 25 13 17 4 458.16 4.00 26 13 42 29 296.43 0.12 27 13 43 30 296.62 0.20 28 13 46 33 296.96 0.37 29 14 17 3 471.16 2.27 30 14 18 4 458.79 3.68 31 14 43 29 296.89 0.33 32 15 18 3 458.80 3.68 33 15 19 4 453.88 1.88 34 16 19 3 459.30 3.93 35 16 20 4 458.63 4.25 36 16 30 14 324.30 5.69 37 16 42 26 296.95 0.34 38 16 65 49 295.08 0.17 39 16 66 50 295.13 0.17 40 16 69 53 291.13 1.11 41 17 20 3 479.27 2.94 42 17 21 4 465.51 0.66 43 17 22 5 440.21 1.59 44 17 23 6 370.52 2.17 45 17 24 7 370.51 2.18 46 17 25 8 363.70 1.14 47 18 22 4 402.91 9.96 48 18 23 5 401.30 10.72 49 19 69 50 291.75 1.31 50 20 25 5 380.59 0.39 51 20 30 10 370.41 2.19 52 20 68 48 294.86 0.10 53 20 69 49 292.60 0.91 54 21 24 3 487.19 0.90 55 21 25 4 393.86 8.68 56 21 26 5 419.55 4.16 57 24 87 63 54.27 0.14 58 25 30 5 449.00 2.41 59 25 39 14 299.29 0.13 60 26 29 3 459.70 2.17 61 26 30 4 456.06 1.07 62 26 85 59 63.63 3.46 63 27 30 3 458.97 2.52 64 27 31 4 449.12 2.40 65 27 37 10 302.49 0.64 66 27 39 12 301.93 0.43 67 27 85 58 67.19 1.71 68 27 89 62 54.45 0.07 69 27 91 64 54.12 0.13 70 28 31 3 459.09 2.58 71 28 32 4 459.09 2.58 72 29 32 3 459.09 2.58 73 29 33 4 459.00 2.63 74 29 68 39 297.83 0.68 75 29 79 50 145.88 17.23 76 29 80 51 144.41 17.95 77 29 81 52 107.84 0.30 78 30 33 3 459.00 2.64 79 30 34 4 450.80 1.46 80 30 35 5 438.23 1.35 81 30 38 8 302.52 0.68 82 30 65 35 297.88 0.66 83 30 68 38 297.77 0.65 84 31 35 4 429.49 3.02 85 31 36 5 384.69 19.37 86 31 37 6 333.57 0.96 87 32 79 47 145.89 17.22 88 32 80 48 204.12 11.89 89 33 68 35 297.87 0.67 90 33 75 42 284.40 0.17 91 33 76 43 284.12 0.24 92 33 77 44 268.44 1.45 93 33 78 45 218.92 4.53 94 33 79 46 145.99 17.18 95 34 64 30 297.90 0.66 96 34 68 34 297.87 0.67 97 35 64 29 297.93 0.65 98 35 65 30 297.92 0.65 99 37 91 54 54.12 0.13 100 38 41 3 465.02 2.15 101 38 91 53 54.09 0.15 102 38 93 55 52.36 0.54 103 39 89 50 54.27 0.14 104 39 90 51 54.13 0.13 105 39 91 52 53.99 0.19 106 40 43 3 466.38 1.88 107 40 44 4 461.63 4.24 108 41 44 3 466.38 1.88 109 41 45 4 461.63 4.23 110 41 61 20 298.70 0.60 111 41 65 24 298.45 0.67 112 41 93 52 44.80 0.88 113 42 45 3 466.38 1.88 114 42 46 4 461.64 4.24 115 42 55 13 298.92 0.65 116 42 61 19 298.72 0.60 117 42 62 20 298.70 0.60 118 42 65 23 298.55 0.65 119 43 46 3 465.10 2.58 120 44 47 3 476.27 1.90 121 44 92 48 50.05 0.69 122 44 93 49 44.80 0.88 123 44 94 50 44.86 0.90 124 45 48 3 519.32 2.90 125 45 55 10 299.08 0.73 126 45 94 49 44.80 0.88 127 46 55 9 299.10 0.73 128 46 62 16 299.08 0.73 129 50 53 3 464.74 2.77 130 53 56 3 483.25 1.32 131 54 59 5 377.46 4.50 132 54 62 8 325.79 8.52 133 55 58 3 472.75 5.03 134 55 59 4 377.47 4.50 135 55 61 6 368.94 0.24 136 55 62 7 342.22 16.73 137 58 61 3 476.70 2.69 138 59 62 3 476.68 2.69 139 59 63 4 465.44 2.33 140 60 63 3 470.37 0.13 141 60 64 4 470.50 0.21 142 61 64 3 470.51 0.21 143 61 65 4 470.51 0.21 144 62 65 3 478.18 4.05 145 62 66 4 465.20 2.87 146 63 66 3 465.20 2.87 147 63 67 4 462.81 1.22 148 64 67 3 468.44 1.59 149 64 68 4 466.47 0.60 150 65 68 3 469.75 0.94 151 65 69 4 462.85 1.22 152 66 69 3 466.56 0.45 153 66 70 4 467.35 1.61 154 67 70 3 467.35 1.61 155 67 71 4 461.39 4.59 156 68 71 3 468.08 1.40 157 71 74 3 497.85 1.02 158 71 75 4 448.84 0.14 159 71 76 5 438.49 3.67 160 72 75 3 488.84 2.50 161 75 78 3 475.19 4.87 162 83 126 43 8.36 1.03 163 83 127 44 8.39 1.02 164 84 127 43 8.40 1.02 165 86 89 3 551.33 1.26 166 92 95 3 474.48 0.52 167 104 140 36 142.12 4.34 168 106 111 5 461.45 0.58 169 106 140 34 142.81 4.13 170 106 142 36 142.26 4.38 171 106 143 37 142.25 4.38 172 107 142 35 142.77 4.13 173 107 143 36 142.72 4.14 174 107 146 39 142.25 4.37 175 108 111 3 463.15 4.41 176 108 112 4 455.30 0.49 177 108 143 35 144.81 3.15 178 109 112 3 456.13 0.67 179 109 113 4 455.30 0.49 180 110 113 3 477.73 2.06 181 110 114 4 455.40 0.54 182 110 137 27 171.48 0.85 183 111 114 3 474.17 3.33 184 111 115 4 455.38 0.55 185 111 133 22 171.61 0.84 186 111 134 23 171.50 0.86 187 111 137 26 171.53 0.84 188 111 138 27 171.53 0.84 189 111 143 32 169.56 1.06 190 112 116 4 453.66 1.38 191 112 146 34 164.93 0.24 192 112 147 35 164.06 0.48 193 113 116 3 457.35 0.69 194 113 117 4 456.67 0.12 195 114 117 3 474.58 2.18 196 114 118 4 461.69 2.38 197 114 133 19 171.72 0.86 198 115 118 3 467.49 0.52 199 115 119 4 470.30 0.88 200 115 129 14 171.81 0.84 201 115 130 15 171.74 0.86 202 115 133 18 171.74 0.86 203 115 144 29 171.09 0.87 204 115 147 32 170.25 0.73 205 115 148 33 169.92 0.57 206 116 119 3 473.45 2.46 207 116 147 31 170.16 0.69 208 117 120 3 483.67 1.82 209 117 121 4 470.30 0.88 210 118 121 3 467.90 2.08 211 118 122 4 457.96 1.35 212 118 123 5 448.69 1.12 213 118 124 6 357.75 2.50 214 118 129 11 172.06 0.86 215 118 147 29 171.17 0.93 216 119 124 5 396.94 6.78 217 119 147 28 171.26 0.88 218 119 151 32 161.02 0.32 219 119 152 33 160.02 0.17 220 122 125 3 563.56 2.35 221 123 126 3 478.12 1.71 222 123 129 6 423.23 2.41 223 124 129 5 456.57 2.25 224 124 148 24 171.31 0.89 225 125 129 4 466.56 2.73 226 126 129 3 463.55 2.79 227 126 130 4 459.53 0.79 228 127 130 3 478.07 3.02 229 127 131 4 459.53 0.79 230 128 131 3 468.53 0.32 231 128 132 4 458.56 1.25 232 129 132 3 458.98 1.35 233 129 133 4 462.62 3.27 234 130 133 3 477.81 4.32 235 130 134 4 460.43 0.62 236 130 144 14 171.91 0.59 237 130 148 18 171.34 0.88 238 131 134 3 460.43 0.62 239 131 135 4 453.58 0.63 240 131 141 10 173.21 0.65 241 131 144 13 172.61 0.90 242 132 135 3 465.75 0.73 243 132 136 4 453.59 0.64 244 133 136 3 453.07 0.91 245 133 137 4 455.28 3.01 246 133 144 11 172.62 0.89 247 134 138 4 415.54 3.60 248 134 139 5 366.56 11.96 249 134 140 6 345.69 2.67 250 134 141 7 181.16 3.22 251 134 143 9 172.88 0.76 252 134 144 10 172.62 0.89 253 135 138 3 434.66 10.11 254 135 139 4 351.53 5.57 255 141 144 3 470.64 7.51 256 141 145 4 463.30 4.18 257 142 145 3 479.45 3.10 258 142 146 4 464.56 4.80 259 143 146 3 468.21 2.98 260 143 147 4 464.62 4.77 261 144 147 3 475.71 1.24 262 144 148 4 452.29 1.39 263 145 148 3 470.24 1.50 264 145 149 4 450.64 0.56 265 146 149 3 481.88 0.27 266 146 150 4 452.91 1.08 267 147 150 3 456.46 2.85 268 147 151 4 438.93 4.55 269 147 152 5 438.41 4.29 270 148 152 4 410.86 1.66 271 149 152 3 464.66 1.25