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 6 3 396.07 1.20 2 3 7 4 389.89 0.32 3 3 55 52 29.18 1.07 4 3 56 53 29.18 1.08 5 4 7 3 395.85 0.64 6 4 8 4 389.89 0.32 7 4 55 51 29.20 1.08 8 4 104 100 31.17 0.10 9 4 107 103 29.20 1.08 10 4 108 104 29.20 1.08 11 4 111 107 29.09 1.04 12 5 8 3 404.01 1.65 13 5 9 4 384.40 2.43 14 5 10 5 367.17 2.27 15 5 11 6 378.47 3.38 16 5 14 9 305.94 3.79 17 5 52 47 29.21 1.08 18 5 55 50 29.21 1.08 19 5 57 52 29.21 1.07 20 6 9 3 403.88 0.70 21 6 10 4 378.47 3.38 22 7 104 97 34.87 0.36 23 7 107 100 34.86 0.36 24 8 13 5 351.64 6.10 25 8 55 47 35.01 0.29 26 8 100 92 35.45 0.10 27 8 104 96 34.88 0.36 28 8 108 100 34.87 0.36 29 9 13 4 368.16 2.16 30 10 13 3 402.00 2.06 31 10 14 4 390.04 0.38 32 11 14 3 406.18 0.32 33 11 15 4 389.81 0.49 34 12 15 3 402.97 0.74 35 12 16 4 396.65 3.90 36 13 16 3 405.00 0.27 37 13 17 4 396.68 3.89 38 13 98 85 77.67 0.21 39 14 17 3 405.01 0.28 40 14 18 4 396.90 3.79 41 14 48 34 65.47 0.02 42 14 51 37 65.39 0.06 43 14 52 38 65.39 0.06 44 14 55 41 65.41 0.05 45 15 18 3 407.33 1.15 46 15 19 4 398.04 3.22 47 15 48 33 68.28 0.17 48 16 19 3 408.44 1.96 49 16 20 4 404.87 0.19 50 16 98 82 89.17 0.01 51 17 20 3 407.34 1.42 52 17 21 4 404.87 0.20 53 17 94 77 81.07 0.12 54 17 95 78 81.84 0.50 55 17 98 81 89.17 0.01 56 18 21 3 402.79 3.69 57 18 22 4 400.24 4.96 58 18 44 26 86.02 1.58 59 18 47 29 79.64 0.81 60 18 48 30 80.61 0.31 61 18 51 33 79.64 0.81 62 19 22 3 408.79 0.69 63 19 23 4 405.86 0.78 64 19 44 25 89.69 0.05 65 19 48 29 89.39 0.10 66 20 23 3 405.86 0.79 67 20 24 4 405.85 0.79 68 20 94 74 89.95 0.01 69 21 24 3 406.43 0.49 70 21 25 4 404.43 1.49 71 21 87 66 89.84 0.01 72 21 90 69 89.89 0.02 73 21 91 70 89.84 0.01 74 21 94 73 90.02 0.04 75 22 25 3 399.79 3.81 76 22 26 4 399.78 3.81 77 22 35 13 209.30 4.12 78 22 40 18 94.77 0.04 79 22 43 21 94.46 0.09 80 22 44 22 94.00 0.24 81 22 47 25 94.12 0.21 82 23 26 3 411.24 2.90 83 23 27 4 400.34 3.54 84 24 27 3 401.30 2.07 85 24 28 4 390.50 0.83 86 24 90 66 94.66 0.06 87 24 93 69 94.69 0.06 88 24 94 70 94.71 0.07 89 24 97 73 94.89 0.06 90 25 28 3 405.08 0.18 91 25 31 6 305.87 6.55 92 25 32 7 245.08 4.21 93 25 35 10 228.54 12.41 94 25 90 65 94.67 0.07 95 26 32 6 245.09 4.22 96 26 35 9 244.94 4.21 97 26 40 14 144.66 24.79 98 27 32 5 309.56 10.84 99 28 31 3 418.54 1.66 100 28 32 4 340.25 1.21 101 28 86 58 94.70 0.07 102 28 90 62 94.73 0.07 103 29 32 3 414.96 1.48 104 30 33 3 525.02 2.01 105 30 83 53 94.65 0.06 106 30 86 56 94.70 0.07 107 30 89 59 94.90 0.08 108 30 90 60 94.91 0.08 109 31 34 3 413.23 0.24 110 31 83 52 94.62 0.05 111 31 86 55 94.69 0.07 112 31 87 56 94.69 0.06 113 31 90 59 94.90 0.07 114 32 35 3 409.26 1.74 115 33 36 3 408.15 1.32 116 34 38 4 413.04 1.11 117 34 73 39 91.89 0.51 118 34 77 43 91.95 0.54 119 34 79 45 92.46 0.30 120 34 83 49 94.64 0.06 121 35 38 3 403.61 3.60 122 35 40 5 351.23 1.17 123 35 43 8 324.58 3.31 124 38 43 5 390.72 0.10 125 39 42 3 404.17 1.58 126 39 43 4 390.78 0.09 127 40 43 3 399.22 1.23 128 40 44 4 390.78 0.09 129 41 44 3 406.87 1.22 130 41 45 4 395.31 1.77 131 42 45 3 412.81 1.33 132 42 46 4 391.55 0.12 133 43 46 3 404.00 3.08 134 43 47 4 392.51 0.10 135 44 47 3 404.34 0.01 136 44 48 4 392.06 0.14 137 45 48 3 406.26 3.34 138 45 49 4 395.69 1.95 139 46 49 3 408.97 1.99 140 46 50 4 391.57 0.12 141 46 61 15 96.02 0.31 142 47 50 3 411.09 0.93 143 47 51 4 390.72 0.55 144 48 51 3 405.45 0.23 145 48 52 4 390.30 0.41 146 49 52 3 406.35 4.61 147 49 53 4 390.32 0.40 148 49 61 12 96.02 0.31 149 50 53 3 402.59 6.50 150 50 54 4 391.31 0.90 151 50 61 11 96.41 0.12 152 50 66 16 95.17 0.18 153 51 54 3 391.35 0.89 154 51 55 4 391.32 0.90 155 51 91 40 96.90 0.14 156 52 55 3 409.87 2.85 157 52 56 4 391.31 0.90 158 52 57 5 321.19 1.72 159 52 58 6 306.07 5.83 160 53 56 3 395.16 0.20 161 53 58 5 306.06 5.83 162 53 59 6 268.85 12.78 163 53 60 7 209.23 0.48 164 53 61 8 97.06 0.07 165 54 111 57 96.61 0.29 166 55 108 53 97.12 0.06 167 55 111 56 96.89 0.15 168 61 64 3 513.18 1.38 169 64 68 4 395.42 0.44 170 64 69 5 371.32 1.31 171 65 68 3 410.36 0.28 172 65 69 4 384.07 1.61 173 66 69 3 402.87 3.28 174 66 70 4 395.50 0.41 175 66 117 51 178.83 6.28 176 66 120 54 178.77 6.25 177 66 121 55 178.80 6.27 178 67 70 3 403.44 0.92 179 67 71 4 384.07 1.61 180 67 119 52 178.83 6.28 181 67 120 53 178.78 6.26 182 67 123 56 178.71 6.29 183 67 124 57 178.72 6.28 184 68 71 3 395.50 0.41 185 70 73 3 406.52 4.03 186 70 74 4 394.79 0.14 187 70 79 9 226.86 0.94 188 70 121 51 178.84 6.27 189 70 123 53 178.84 6.27 190 71 74 3 400.00 1.34 191 71 75 4 395.92 0.71 192 71 123 52 178.84 6.27 193 72 75 3 407.33 6.32 194 72 76 4 392.14 1.18 195 72 77 5 384.75 4.87 196 73 77 4 363.03 5.23 197 73 78 5 349.10 12.19 198 73 79 6 285.93 21.05 199 74 79 5 241.67 1.07 200 74 121 47 179.13 6.25 201 74 122 48 179.09 6.24 202 74 123 49 179.01 6.20 203 78 83 5 395.71 0.43 204 79 83 4 395.70 0.43 205 79 121 42 180.34 6.38 206 79 122 43 179.52 6.39 207 80 83 3 398.45 0.36 208 80 84 4 395.70 0.43 209 80 122 42 179.81 6.24 210 81 84 3 395.72 0.43 211 81 85 4 395.70 0.42 212 81 118 37 180.58 6.32 213 81 122 41 180.44 6.33 214 82 85 3 411.56 2.91 215 82 86 4 395.70 0.42 216 83 86 3 405.26 3.71 217 83 87 4 397.64 0.55 218 84 87 3 402.79 1.82 219 84 88 4 397.45 0.84 220 84 112 28 182.10 6.12 221 84 113 29 182.03 6.16 222 84 117 33 181.69 6.06 223 84 118 34 180.57 6.29 224 84 121 37 180.52 6.30 225 84 122 38 180.50 6.30 226 85 88 3 409.06 1.31 227 85 89 4 392.50 1.64 228 86 89 3 404.03 3.83 229 86 90 4 395.22 0.28 230 87 90 3 409.11 1.28 231 87 91 4 396.05 0.17 232 88 91 3 409.11 1.28 233 88 92 4 405.51 3.08 234 88 112 24 182.12 6.13 235 89 92 3 406.82 2.42 236 89 93 4 398.78 0.29 237 90 93 3 404.04 3.83 238 90 94 4 398.31 2.44 239 91 94 3 400.24 1.51 240 91 95 4 398.42 2.42 241 91 108 17 183.63 5.91 242 91 112 21 183.29 5.87 243 92 95 3 400.57 1.34 244 92 96 4 398.33 2.46 245 92 105 13 183.64 5.90 246 92 108 16 183.63 5.90 247 92 109 17 183.46 5.87 248 93 96 3 398.72 2.27 249 93 97 4 398.32 2.47 250 94 97 3 401.30 0.97 251 94 98 4 398.30 2.46 252 95 98 3 399.55 0.66 253 95 99 4 393.81 0.23 254 95 100 5 370.11 5.91 255 95 105 10 191.37 3.12 256 95 108 13 184.95 5.84 257 96 99 3 402.46 2.12 258 96 102 6 342.17 10.16 259 96 105 9 212.50 7.42 260 100 104 4 385.82 3.27 261 100 105 5 385.68 3.20 262 101 104 3 407.89 0.94 263 101 105 4 386.47 3.58 264 102 105 3 395.45 0.91 265 102 106 4 386.48 3.58 266 103 106 3 403.30 3.54 267 103 107 4 385.90 3.29 268 104 107 3 398.70 0.19 269 104 108 4 386.23 3.44 270 105 108 3 397.32 2.08 271 105 109 4 386.26 3.45 272 106 109 3 397.33 2.08 273 106 110 4 396.18 1.51 274 107 110 3 412.88 4.99 275 107 111 4 396.44 1.39 276 108 111 3 412.07 5.40 277 108 112 4 390.39 1.36 278 109 112 3 406.93 2.83 279 109 113 4 389.03 1.42 280 110 113 3 406.94 2.83 281 110 114 4 389.03 1.43 282 111 114 3 407.63 2.48 283 111 117 6 335.07 3.85 284 112 117 5 335.07 3.85 285 114 117 3 396.00 1.61 286 114 118 4 379.82 6.48 287 115 118 3 391.33 1.54 288 115 119 4 377.42 7.78 289 116 120 4 391.12 1.34 290 117 120 3 400.19 0.24 291 117 121 4 397.87 0.83 292 118 121 3 401.84 0.58 293 118 122 4 391.13 1.35 294 119 122 3 404.02 1.67 295 119 123 4 383.09 4.90 296 119 124 5 304.34 1.46 297 120 123 3 399.82 1.59