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 4 86 82 231.00 44.09 2 5 9 4 819.28 4.30 3 5 78 73 230.68 44.23 4 8 11 3 839.13 0.26 5 8 12 4 780.19 9.21 6 9 13 4 778.94 9.85 7 10 14 4 808.93 5.95 8 10 71 61 243.12 40.82 9 10 75 65 243.34 40.81 10 10 78 68 243.37 40.83 11 10 100 90 242.13 41.53 12 10 178 168 150.13 0.46 13 10 182 172 139.55 3.12 14 11 15 4 771.77 2.62 15 11 178 167 150.04 0.50 16 11 182 171 139.64 3.10 17 12 16 4 773.33 3.56 18 13 17 4 793.19 6.37 19 14 18 4 791.54 7.19 20 14 67 53 244.11 40.43 21 14 71 57 244.26 40.50 22 14 108 94 244.19 40.47 23 14 174 160 155.13 2.25 24 14 178 164 154.89 2.33 25 15 19 4 770.24 3.46 26 16 20 4 770.24 3.46 27 17 21 4 755.73 2.53 28 17 67 50 245.53 40.48 29 18 22 4 782.46 2.61 30 18 64 46 245.52 40.49 31 18 67 49 245.53 40.49 32 18 108 90 245.38 40.49 33 18 170 152 170.88 4.13 34 18 174 156 156.62 2.98 35 19 23 4 783.09 2.30 36 20 24 4 782.86 2.41 37 21 24 3 829.15 4.54 38 21 25 4 778.51 0.01 39 21 63 42 245.58 40.50 40 22 25 3 823.89 7.18 41 22 26 4 772.88 2.29 42 22 167 145 175.50 5.51 43 22 170 148 175.12 5.71 44 23 27 4 787.25 4.54 45 24 28 4 799.81 1.74 46 25 28 3 815.94 5.03 47 25 29 4 803.40 3.52 48 26 30 4 819.08 2.83 49 26 163 137 187.89 6.12 50 27 30 3 819.11 2.82 51 27 31 4 819.08 2.83 52 28 31 3 831.81 3.18 53 28 32 4 806.51 3.46 54 29 32 3 814.30 1.81 55 29 33 4 806.50 3.46 56 29 55 26 252.73 37.36 57 29 56 27 252.20 37.61 58 29 59 30 252.21 37.56 59 29 163 134 188.62 5.76 60 30 34 4 798.40 3.67 61 30 160 130 188.72 5.79 62 31 35 4 751.95 0.62 63 32 36 4 738.05 6.32 64 33 37 4 723.70 13.50 65 33 52 19 253.13 37.27 66 33 156 123 193.19 7.29 67 33 159 126 193.16 7.29 68 34 38 4 724.01 4.01 69 34 156 122 193.18 7.28 70 34 160 126 193.18 7.28 71 36 40 4 725.51 1.59 72 37 40 3 799.57 2.44 73 37 152 115 205.54 0.12 74 37 156 119 194.30 6.79 75 38 152 114 205.57 0.14 76 38 156 118 206.61 0.66 77 40 43 3 846.50 3.21 78 40 48 8 571.03 1.30 79 43 148 105 292.36 43.16 80 43 151 108 293.50 42.59 81 44 48 4 802.40 2.06 82 46 50 4 735.79 4.08 83 46 51 5 739.67 2.14 84 47 51 4 739.67 2.14 85 47 52 5 758.90 4.79 86 48 52 4 796.01 5.17 87 48 155 107 295.89 43.94 88 49 53 4 825.58 0.10 89 49 127 78 354.54 14.73 90 49 130 81 354.58 14.70 91 50 53 3 826.03 0.32 92 50 54 4 803.16 1.59 93 51 55 4 806.43 3.22 94 52 55 3 825.25 0.07 95 52 56 4 814.50 0.82 96 52 159 107 295.98 44.12 97 53 57 4 814.50 0.82 98 53 123 70 354.97 14.54 99 53 127 74 355.44 14.80 100 54 57 3 814.50 0.82 101 54 58 4 795.26 4.84 102 55 58 3 838.86 0.26 103 55 59 4 795.22 4.82 104 56 60 4 796.58 4.12 105 56 166 110 292.35 46.12 106 57 61 4 766.58 5.12 107 57 119 62 355.23 14.61 108 57 123 66 355.48 14.77 109 58 62 4 759.37 8.72 110 59 63 4 751.39 9.83 111 60 64 4 773.55 0.96 112 60 115 55 358.01 13.57 113 60 166 106 292.61 46.26 114 61 116 55 358.23 13.60 115 62 66 4 831.63 1.91 116 63 66 3 861.52 2.08 117 63 67 4 831.63 1.91 118 64 67 3 833.82 0.82 119 64 68 4 817.41 0.55 120 64 108 44 359.49 13.18 121 64 115 51 358.84 13.91 122 65 68 3 842.18 5.32 123 65 69 4 815.44 0.44 124 66 69 3 814.94 1.49 125 66 70 4 810.53 2.76 126 67 71 4 782.98 6.86 127 68 72 4 773.48 2.10 128 68 108 40 359.66 13.25 129 69 73 4 765.32 3.73 130 70 74 4 764.00 3.08 131 71 75 4 768.08 4.87 132 71 104 33 362.67 12.97 133 71 178 107 268.44 59.05 134 72 76 4 793.31 4.78 135 72 104 32 362.66 12.97 136 72 105 33 362.63 12.99 137 72 108 36 362.54 13.03 138 73 77 4 808.35 2.74 139 74 78 4 810.44 2.15 140 75 78 3 816.88 0.29 141 75 79 4 814.28 0.24 142 75 100 25 363.11 12.90 143 75 104 29 362.83 13.01 144 76 79 3 823.67 2.38 145 76 80 4 814.29 0.24 146 77 81 4 782.34 2.93 147 78 82 4 781.11 2.29 148 79 83 4 805.50 4.32 149 80 83 3 821.19 2.37 150 81 86 5 754.64 1.32 151 82 86 4 716.19 17.90 152 82 87 5 716.19 17.90 153 82 88 6 604.88 9.11 154 83 88 5 627.75 2.40 155 83 93 10 403.95 1.17 156 89 92 3 841.59 0.62 157 89 189 100 189.22 54.13 158 90 93 3 875.98 0.10 159 92 95 3 817.25 8.84 160 92 96 4 799.50 7.24 161 92 189 97 193.13 52.16 162 93 97 4 807.83 3.07 163 94 98 4 817.51 4.59 164 95 99 4 829.27 2.74 165 96 99 3 846.47 2.56 166 96 100 4 810.44 1.12 167 96 189 93 195.16 50.86 168 97 101 4 810.43 1.13 169 98 102 4 783.84 3.77 170 99 103 4 780.77 2.28 171 99 181 82 268.37 59.13 172 100 104 4 777.55 3.90 173 100 181 81 267.67 59.20 174 101 105 4 766.27 1.74 175 102 106 4 751.25 5.77 176 103 107 4 759.56 1.16 177 103 177 74 268.66 59.06 178 103 181 78 268.50 59.07 179 104 108 4 760.39 0.74 180 104 181 77 268.50 59.07 181 105 109 4 763.59 0.86 182 106 110 4 785.17 4.85 183 107 111 4 813.96 6.71 184 107 173 66 269.36 58.88 185 107 177 70 269.14 58.95 186 108 111 3 816.62 5.40 187 108 112 4 813.98 6.72 188 108 174 66 269.41 58.91 189 109 112 3 816.63 5.40 190 109 113 4 816.64 5.40 191 110 113 3 816.64 5.40 192 110 114 4 813.98 6.74 193 111 115 4 817.66 4.89 194 111 170 59 293.20 47.36 195 111 173 62 292.76 47.30 196 111 174 63 292.86 47.24 197 112 115 3 821.50 2.98 198 112 116 4 817.66 4.88 199 113 117 4 809.64 0.88 200 114 117 3 809.64 0.88 201 114 118 4 783.75 3.04 202 115 119 4 790.75 0.47 203 115 166 51 294.83 47.66 204 115 170 55 294.80 47.65 205 116 120 4 814.87 1.79 206 117 121 4 837.95 1.26 207 118 121 3 851.47 3.52 208 118 122 4 836.58 1.95 209 118 165 47 295.57 47.73 210 118 166 48 295.56 47.73 211 118 169 51 295.54 47.73 212 119 122 3 836.59 1.95 213 119 123 4 819.13 3.97 214 119 166 47 295.57 47.73 215 120 123 3 837.98 1.25 216 120 124 4 815.81 2.31 217 121 124 3 834.97 0.06 218 121 125 4 802.16 4.60 219 121 162 41 297.09 47.15 220 122 125 3 830.23 2.31 221 122 126 4 789.70 1.18 222 122 159 37 298.38 46.58 223 122 162 40 296.44 47.48 224 122 166 44 296.15 47.65 225 123 127 4 788.84 1.59 226 124 128 4 781.96 5.03 227 125 129 4 768.59 7.87 228 126 130 4 786.01 0.84 229 126 154 28 300.21 46.06 230 126 155 29 300.21 46.07 231 126 158 32 299.95 46.15 232 126 159 33 300.00 46.13 233 127 131 4 797.24 2.74 234 128 131 3 817.97 1.46 235 128 132 4 797.23 2.73 236 129 133 4 797.23 2.74 237 130 134 4 780.81 10.95 238 131 135 4 742.71 6.50 239 132 136 4 744.93 3.24 240 133 137 4 744.94 3.23 241 133 138 5 717.42 10.52 242 134 138 4 698.90 1.94 243 134 151 17 300.60 46.06 244 138 147 9 416.93 17.70 245 141 146 5 811.21 1.72 246 144 147 3 841.87 5.89 247 144 148 4 796.38 4.07 248 145 148 3 838.31 3.39 249 145 149 4 802.64 1.68 250 146 149 3 836.73 4.17 251 146 150 4 801.89 1.31 252 147 150 3 832.25 1.50 253 147 151 4 802.53 0.47 254 148 152 4 779.90 2.79 255 149 153 4 775.52 1.90 256 150 154 4 769.37 4.97 257 151 155 4 773.75 2.77 258 152 156 4 778.42 3.17 259 153 157 4 765.60 3.97 260 154 158 4 769.64 1.95 261 155 159 4 776.16 1.31 262 156 160 4 752.25 10.64 263 157 161 4 763.82 4.87 264 158 162 4 773.52 2.57 265 159 163 4 784.75 3.04 266 161 165 4 838.57 3.54 267 162 165 3 845.18 3.71 268 162 166 4 838.57 3.54 269 163 166 3 848.16 3.89 270 163 167 4 813.49 1.04 271 164 167 3 831.00 1.07 272 164 168 4 804.81 2.67 273 165 169 4 796.25 1.21 274 166 170 4 779.75 7.05 275 167 171 4 802.15 1.07 276 168 171 3 841.07 5.09 277 168 172 4 799.08 2.60 278 169 172 3 814.06 0.30 279 169 173 4 783.76 0.64 280 170 174 4 783.76 0.64 281 171 175 4 776.51 3.54 282 172 176 4 757.40 4.51 283 173 177 4 787.20 2.75 284 174 178 4 783.00 0.03 285 175 179 4 793.40 1.68 286 176 179 3 822.77 4.73 287 176 180 4 791.14 0.55 288 177 181 4 791.12 0.54 289 178 182 4 769.86 11.17 290 179 183 4 757.88 3.60 291 180 184 4 753.78 1.55 292 181 185 4 703.59 1.28 293 182 186 4 727.14 10.50 294 183 187 4 748.65 0.26 295 184 188 4 772.00 4.80 296 184 199 15 132.82 26.99 297 185 189 4 801.42 3.62 298 187 198 11 289.30 51.15 299 188 192 4 763.51 11.02 300 188 193 5 499.49 5.83 301 191 194 3 848.17 3.29 302 193 240 47 47.00 0.63 303 194 198 4 835.21 0.61 304 194 240 46 47.93 0.23 305 195 198 3 831.44 2.50 306 195 199 4 789.01 2.07 307 195 239 44 48.31 0.24 308 195 240 45 48.16 0.23 309 196 200 4 800.11 1.00 310 196 236 40 48.34 0.22 311 196 240 44 48.28 0.26 312 198 202 4 770.56 5.92 313 199 203 4 775.14 8.22 314 200 204 4 792.99 0.70 315 200 233 33 53.44 0.28 316 200 236 36 53.38 0.25 317 201 204 3 827.10 2.02 318 201 205 4 788.99 2.71 319 202 206 4 803.12 5.73 320 203 207 4 803.37 3.55 321 203 229 26 55.55 0.03 322 204 208 4 815.87 2.69 323 204 229 25 55.55 0.03 324 205 209 4 830.40 0.41 325 206 209 3 847.62 1.26 326 206 210 4 820.86 5.17 327 207 211 4 803.08 1.42 328 207 225 18 63.73 2.63 329 208 212 4 793.37 5.33 330 209 213 4 790.25 6.90 331 210 214 4 791.70 2.31 332 211 214 3 823.99 4.58 333 211 221 10 206.77 7.51 334 211 225 14 155.34 33.52 335 216 220 4 816.16 0.58 336 216 221 5 791.71 3.16 337 218 221 3 817.78 0.36 338 218 222 4 809.36 3.99 339 219 222 3 865.68 2.64 340 219 223 4 803.35 1.00 341 220 224 4 778.28 5.44 342 221 225 4 764.52 1.45 343 222 226 4 781.85 0.23 344 223 227 4 795.15 3.71 345 224 228 4 793.25 4.67 346 225 228 3 805.44 3.61 347 225 229 4 793.25 4.67 348 226 230 4 797.78 2.39 349 227 230 3 820.65 1.86 350 227 231 4 787.84 0.55 351 228 231 3 821.85 1.50 352 228 232 4 787.84 0.55 353 229 233 4 787.84 0.55 354 230 234 4 799.58 5.32 355 231 235 4 799.21 5.50 356 232 236 4 806.66 1.78 357 233 236 3 836.34 2.85 358 233 237 4 806.66 1.78 359 234 238 4 773.38 6.09 360 235 239 4 773.38 6.09 361 236 239 3 812.53 4.84 362 236 240 4 767.25 9.15 363 237 241 4 782.64 0.20 364 238 242 4 782.04 10.42 365 239 243 4 751.72 6.66