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 7 57 50 104.84 2.69 2 7 58 51 104.78 2.71 3 8 11 3 389.04 0.06 4 8 12 4 381.77 3.19 5 8 57 49 104.84 2.69 6 8 58 50 111.67 0.71 7 8 106 98 23.96 0.34 8 8 109 101 22.81 0.23 9 9 12 3 391.44 0.93 10 9 13 4 371.50 0.71 11 9 14 5 371.58 0.77 12 9 17 8 343.60 2.98 13 9 54 45 104.85 2.69 14 9 57 48 104.84 2.69 15 9 59 50 104.86 2.69 16 11 106 95 32.66 0.34 17 12 16 4 364.32 0.11 18 12 17 5 361.00 0.63 19 12 20 8 344.82 2.52 20 12 57 45 137.76 1.91 21 12 106 94 33.19 0.09 22 13 16 3 391.50 0.64 23 13 17 4 371.43 0.48 24 14 17 3 389.88 1.55 25 14 18 4 372.72 1.12 26 15 18 3 388.54 0.89 27 15 19 4 374.72 1.16 28 16 19 3 380.31 3.96 29 16 20 4 369.52 1.44 30 16 100 84 83.81 3.56 31 17 20 3 388.94 3.66 32 17 21 4 376.41 0.31 33 17 50 33 140.22 2.77 34 17 53 36 140.25 2.77 35 17 54 37 140.24 2.77 36 17 57 40 140.83 2.54 37 18 21 3 389.75 3.25 38 18 22 4 375.55 1.54 39 18 50 32 140.37 2.71 40 19 22 3 394.22 0.92 41 19 23 4 377.15 0.73 42 19 100 81 89.46 0.91 43 20 23 3 390.42 0.99 44 20 24 4 381.97 3.10 45 20 93 73 90.95 0.65 46 20 96 76 90.50 0.60 47 20 97 77 90.13 0.78 48 20 100 80 89.48 0.92 49 20 102 82 89.33 0.84 50 20 110 90 88.20 0.71 51 21 24 3 377.86 0.47 52 21 25 4 376.33 0.29 53 21 46 25 141.58 2.48 54 21 49 28 141.41 2.42 55 21 50 29 141.41 2.42 56 21 53 32 141.41 2.42 57 22 25 3 377.86 0.38 58 22 26 4 377.16 0.12 59 22 46 24 141.68 2.50 60 22 50 28 141.67 2.50 61 23 26 3 384.75 3.83 62 23 27 4 377.14 0.14 63 23 96 73 90.52 0.59 64 23 99 76 90.06 0.79 65 23 100 77 89.94 0.83 66 24 27 3 379.89 1.25 67 24 28 4 368.45 4.46 68 24 89 65 91.24 0.59 69 24 92 68 91.14 0.58 70 24 93 69 90.97 0.66 71 24 96 72 90.53 0.59 72 25 28 3 381.47 5.54 73 25 29 4 376.03 8.26 74 25 38 13 152.92 2.93 75 25 42 17 142.10 2.40 76 25 45 20 142.08 2.41 77 25 46 21 141.99 2.38 78 25 49 24 141.97 2.37 79 26 29 3 391.42 0.57 80 26 30 4 374.06 9.24 81 27 30 3 382.88 4.83 82 27 31 4 370.94 10.80 83 27 92 65 91.23 0.60 84 27 95 68 91.22 0.60 85 27 99 72 91.17 0.60 86 28 31 3 376.43 0.42 87 28 34 6 215.11 11.03 88 28 35 7 192.82 3.16 89 28 38 10 159.45 0.29 90 28 42 14 145.74 1.16 91 28 92 64 91.23 0.60 92 29 35 6 192.82 3.16 93 29 42 13 145.73 1.17 94 31 34 3 397.71 2.29 95 31 35 4 357.28 3.62 96 31 88 57 94.80 0.39 97 31 92 61 91.58 0.51 98 32 36 4 380.68 0.67 99 33 36 3 413.55 2.28 100 33 84 51 95.83 0.27 101 33 85 52 95.50 0.42 102 33 88 55 95.29 0.34 103 34 37 3 400.54 0.88 104 34 38 4 379.80 1.11 105 34 85 51 95.48 0.42 106 34 88 54 95.28 0.34 107 34 89 55 94.95 0.48 108 34 92 58 94.61 0.64 109 35 38 3 392.36 4.96 110 37 80 43 96.24 0.42 111 37 85 48 95.73 0.54 112 38 42 4 384.17 0.91 113 38 45 7 270.16 10.14 114 39 42 3 392.29 1.71 115 39 45 6 328.29 0.47 116 42 45 3 380.06 1.09 117 42 46 4 375.06 3.60 118 43 46 3 389.97 1.26 119 43 47 4 379.88 1.20 120 44 47 3 386.41 2.06 121 44 48 4 379.39 1.44 122 45 48 3 386.42 2.06 123 45 49 4 379.39 1.44 124 46 49 3 391.70 0.58 125 46 50 4 379.40 1.44 126 47 50 3 391.71 0.58 127 47 51 4 384.04 1.00 128 47 66 19 219.58 5.84 129 47 67 20 219.53 5.83 130 48 51 3 388.38 1.17 131 48 52 4 372.47 2.04 132 48 63 15 219.54 5.77 133 48 67 19 219.46 5.81 134 49 52 3 376.68 0.06 135 49 53 4 370.64 3.13 136 50 53 3 382.67 3.46 137 50 54 4 370.66 3.15 138 51 54 3 381.17 0.27 139 51 55 4 378.47 0.76 140 51 62 11 219.58 5.79 141 51 63 12 219.55 5.77 142 51 66 15 219.71 5.88 143 51 67 16 219.69 5.88 144 52 55 3 381.25 1.59 145 52 56 4 370.66 3.15 146 52 63 11 219.55 5.77 147 52 70 18 219.37 5.84 148 52 72 20 217.03 5.08 149 53 56 3 378.25 0.10 150 53 57 4 370.65 3.15 151 53 114 61 85.91 0.35 152 54 57 3 390.03 1.21 153 54 58 4 371.53 2.68 154 54 59 5 319.88 2.33 155 54 60 6 312.03 6.25 156 54 62 8 220.47 5.79 157 55 58 3 381.60 3.35 158 55 60 5 281.64 8.95 159 55 61 6 220.46 5.79 160 55 62 7 220.47 5.79 161 55 63 8 220.46 5.79 162 55 64 9 220.46 5.79 163 55 70 15 219.55 5.87 164 56 110 54 87.39 0.61 165 56 113 57 86.25 0.25 166 56 114 58 86.09 0.27 167 56 117 61 84.32 0.36 168 57 106 49 87.53 0.57 169 57 109 52 87.15 0.51 170 57 110 53 87.09 0.48 171 61 64 3 391.25 0.23 172 61 65 4 376.06 3.70 173 62 65 3 382.97 0.25 174 62 66 4 379.11 2.18 175 63 66 3 385.34 0.93 176 63 67 4 374.56 4.46 177 63 68 5 368.12 1.26 178 63 70 7 268.46 7.75 179 63 75 12 265.78 9.09 180 64 67 3 385.37 0.95 181 64 68 4 321.06 9.50 182 64 69 5 320.62 9.71 183 64 70 6 310.81 13.42 184 67 75 8 357.04 3.12 185 69 75 6 384.17 2.31 186 70 75 5 384.18 2.31 187 71 74 3 390.19 1.54 188 71 75 4 388.00 0.42 189 72 75 3 394.77 1.84 190 72 76 4 388.00 0.42 191 72 117 45 81.75 0.23 192 72 121 49 79.75 0.05 193 73 76 3 395.09 2.00 194 73 77 4 393.75 2.37 195 73 120 47 79.83 0.03 196 73 121 48 79.75 0.05 197 73 122 49 79.75 0.05 198 73 123 50 79.75 0.05 199 74 77 3 399.04 0.03 200 74 78 4 402.87 0.85 201 75 78 3 431.01 4.07 202 75 79 4 408.37 0.58 203 76 79 3 402.87 0.85 204 76 81 5 373.81 0.82 205 76 121 45 79.76 0.06 206 76 123 47 79.65 0.04 207 77 123 46 79.39 0.16 208 79 123 44 79.38 0.17 209 80 85 5 371.87 1.02 210 81 85 4 371.87 1.02 211 81 121 40 79.36 0.16 212 81 122 41 78.90 0.01 213 81 123 42 78.67 0.10 214 82 85 3 376.50 1.29 215 82 86 4 371.94 0.98 216 82 122 40 78.67 0.10 217 83 86 3 381.16 1.01 218 83 87 4 373.68 2.05 219 83 122 39 78.09 0.14 220 84 87 3 380.27 0.58 221 84 88 4 373.68 2.05 222 85 88 3 381.64 1.27 223 85 89 4 374.35 2.39 224 86 89 3 381.62 1.26 225 86 90 4 380.04 1.13 226 86 118 32 79.43 0.18 227 86 122 36 77.23 0.24 228 87 90 3 380.00 1.15 229 87 91 4 372.25 2.72 230 88 91 3 385.95 4.13 231 88 92 4 371.00 0.12 232 89 92 3 384.66 4.78 233 89 93 4 383.65 5.29 234 89 114 25 85.52 0.16 235 90 93 3 384.82 4.70 236 90 94 4 384.66 4.78 237 90 111 21 88.20 0.70 238 90 114 24 85.50 0.17 239 90 115 25 85.34 0.19 240 90 118 28 79.70 0.05 241 91 94 3 387.60 3.31 242 91 95 4 384.91 4.65 243 92 95 3 386.19 4.01 244 92 96 4 378.12 0.01 245 93 96 3 378.25 0.04 246 93 97 4 378.13 0.01 247 93 111 18 88.20 0.70 248 93 114 21 85.50 0.17 249 94 97 3 378.70 0.24 250 94 98 4 380.01 0.42 251 94 107 13 191.21 12.85 252 94 111 17 88.21 0.70 253 95 98 3 384.22 1.69 254 95 99 4 380.01 0.42 255 96 99 3 385.87 0.86 256 96 100 4 378.69 0.24 257 97 100 3 385.81 2.48 258 97 101 4 371.05 0.64 259 97 102 5 283.54 13.59 260 97 107 10 196.46 10.22 261 97 111 14 159.81 2.77 262 98 101 3 367.98 0.80 263 98 107 9 269.48 6.08 264 102 106 4 393.15 0.96 265 102 107 5 358.76 5.90 266 102 110 8 344.10 5.42 267 103 106 3 427.12 1.55 268 103 107 4 363.71 8.08 269 104 107 3 402.31 3.25 270 104 108 4 384.38 0.15 271 105 108 3 392.81 1.49 272 105 109 4 384.24 0.07 273 106 109 3 389.79 0.03 274 106 110 4 368.55 6.26 275 107 110 3 389.80 0.03 276 107 111 4 358.47 1.22 277 108 112 4 353.60 7.03 278 109 112 3 385.35 0.32 279 109 113 4 370.69 6.92 280 110 113 3 391.00 0.59 281 110 114 4 373.08 5.73 282 111 114 3 382.23 1.25 283 111 115 4 382.48 1.03 284 112 115 3 390.32 4.96 285 112 116 4 384.72 2.13 286 113 116 3 384.72 2.13 287 113 117 4 385.18 0.12 288 114 117 3 385.20 0.11 289 114 118 4 385.18 0.12 290 115 118 3 389.81 2.31 291 115 119 4 382.80 1.18 292 116 119 3 387.20 0.88 293 116 120 4 382.44 1.37 294 117 120 3 385.31 0.07 295 117 121 4 376.88 4.16 296 118 121 3 382.77 1.21 297 118 122 4 382.77 1.21 298 119 122 3 386.44 3.04