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 18 45 27 62.09 0.27 2 18 46 28 62.09 0.27 3 18 47 29 62.06 0.25 4 18 48 30 55.43 1.02 5 18 49 31 56.84 0.35 6 18 53 35 41.80 0.72 7 19 46 27 62.11 0.27 8 19 47 28 62.09 0.27 9 20 47 27 63.61 0.28 10 20 48 28 62.30 0.19 11 20 60 40 62.27 0.18 12 20 70 50 62.27 0.18 13 20 71 51 63.07 0.54 14 20 72 52 63.08 0.54 15 21 24 3 363.79 2.95 16 21 25 4 281.52 28.66 17 21 47 26 64.17 0.11 18 21 71 50 63.40 0.38 19 22 25 3 355.18 7.26 20 22 26 4 160.27 3.52 21 22 69 47 63.76 0.20 22 22 70 48 64.14 0.12 23 22 71 49 64.20 0.10 24 23 26 3 355.52 8.35 25 23 35 12 64.20 0.10 26 23 37 14 65.47 0.10 27 23 69 46 64.20 0.10 28 23 71 48 64.44 0.03 29 23 101 78 66.95 0.30 30 23 104 81 68.77 1.20 31 23 105 82 66.67 0.28 32 23 108 85 68.77 1.22 33 24 71 47 65.47 0.10 34 24 101 77 68.77 1.16 35 24 104 80 69.42 1.48 36 24 108 84 93.37 13.46 37 26 69 43 65.88 0.07 38 26 108 82 135.25 5.18 39 27 30 3 357.67 1.76 40 27 31 4 327.86 5.96 41 27 69 42 522.65 8.77 42 28 31 3 355.87 4.22 43 28 108 80 134.86 5.38 44 32 112 80 451.57 0.18 45 33 112 79 451.57 0.18 46 33 113 80 451.56 0.18 47 33 211 178 36.49 0.07 48 34 113 79 451.58 0.18 49 34 115 81 451.56 0.18 50 34 207 173 80.05 0.67 51 34 211 177 36.44 0.05 52 35 112 77 524.69 1.18 53 35 113 78 457.94 1.80 54 35 114 79 451.57 0.18 55 35 115 80 451.58 0.18 56 36 115 79 451.58 0.18 57 36 116 80 451.57 0.18 58 36 117 81 451.57 0.18 59 36 203 167 100.66 0.24 60 37 115 78 452.05 0.27 61 37 116 79 451.59 0.18 62 37 117 80 451.58 0.18 63 38 117 79 451.59 0.18 64 38 118 80 451.57 0.18 65 38 119 81 451.57 0.18 66 38 147 109 312.55 0.48 67 39 117 78 451.83 0.26 68 39 118 79 451.57 0.18 69 39 119 80 451.57 0.18 70 39 122 83 364.38 1.18 71 39 125 86 363.67 1.39 72 40 119 79 451.60 0.18 73 40 122 82 364.50 1.12 74 41 119 78 451.71 0.23 75 41 120 79 451.59 0.18 76 42 121 79 451.60 0.18 77 44 119 75 451.89 0.26 78 51 119 68 451.55 0.18 79 51 147 96 312.01 0.68 80 51 191 140 112.88 0.13 81 51 192 141 112.48 0.01 82 51 195 144 108.46 1.17 83 54 195 141 108.49 1.16 84 54 196 142 108.45 1.17 85 55 147 92 312.02 0.69 86 55 195 140 108.50 1.16 87 55 200 145 107.94 0.98 88 55 203 148 106.93 0.60 89 58 196 138 108.42 1.16 90 58 200 142 107.95 0.98 91 59 115 56 453.38 0.45 92 59 203 144 100.62 0.23 93 59 204 145 99.14 0.12 94 62 204 142 99.16 0.13 95 62 208 146 81.76 0.14 96 63 204 141 99.16 0.13 97 63 207 144 80.42 0.54 98 73 125 52 363.68 1.38 99 77 121 44 451.51 0.21 100 77 122 45 449.31 0.47 101 77 125 48 364.09 1.20 102 79 121 42 451.54 0.21 103 80 121 41 451.72 0.24 104 83 121 38 451.72 0.21 105 84 121 37 451.71 0.21 106 84 182 98 158.41 1.23 107 85 182 97 173.66 1.69 108 87 151 64 310.45 0.49 109 88 124 36 447.15 0.58 110 88 128 40 364.01 1.27 111 88 131 43 363.62 1.38 112 88 132 44 363.61 1.37 113 88 151 63 296.82 0.91 114 89 121 32 451.56 0.21 115 89 124 35 400.79 1.59 116 89 151 62 296.83 0.91 117 90 121 31 451.54 0.18 118 90 125 35 364.79 0.96 119 94 125 31 363.72 1.40 120 95 125 30 363.69 1.38 121 95 128 33 360.70 0.71 122 95 129 34 337.31 0.50 123 95 132 37 329.76 1.89 124 98 125 27 363.69 1.40 125 98 126 28 363.44 1.45 126 98 129 31 335.04 0.67 127 99 129 30 335.04 0.68 128 99 132 33 328.62 1.61 129 99 133 34 315.06 0.42 130 102 114 12 525.80 4.25 131 102 116 14 451.80 0.28 132 102 129 27 335.04 0.67 133 102 130 28 329.75 1.93 134 102 133 31 314.22 0.84 135 102 137 35 313.99 0.83 136 102 141 39 313.81 0.89 137 103 137 34 313.98 0.83 138 105 114 9 466.85 1.02 139 106 137 31 313.95 0.81 140 106 140 34 313.79 0.89 141 109 112 3 451.56 0.18 142 110 140 30 313.75 0.90 143 111 211 100 40.62 0.82 144 113 142 29 313.62 0.85 145 113 207 94 80.08 0.65 146 113 210 97 40.60 0.83 147 113 211 98 37.67 0.64 148 114 137 23 314.06 0.86 149 114 140 26 313.78 0.89 150 114 141 27 313.68 0.88 151 114 142 28 313.67 0.88 152 115 141 26 313.76 0.89 153 115 142 27 313.69 0.88 154 115 143 28 313.55 0.86 155 115 203 88 100.67 0.24 156 115 207 92 80.49 0.56 157 116 130 14 329.75 1.93 158 116 141 25 313.84 0.88 159 116 143 27 313.68 0.88 160 116 144 28 313.29 0.84 161 116 145 29 313.27 0.85 162 117 144 27 313.64 0.87 163 117 145 28 313.28 0.84 164 118 122 4 365.53 0.65 165 118 123 5 364.35 1.18 166 118 126 8 363.31 1.51 167 118 145 27 313.64 0.87 168 118 146 28 313.19 0.80 169 118 147 29 312.19 0.64 170 119 122 3 366.78 1.25 171 119 123 4 365.54 0.65 172 119 147 28 312.09 0.70 173 119 188 69 116.22 1.51 174 119 189 70 116.10 1.46 175 119 191 72 112.91 0.12 176 120 123 3 369.90 1.84 177 120 124 4 368.07 1.90 178 120 147 27 313.47 0.91 179 120 148 28 312.05 0.67 180 120 150 30 303.68 1.98 181 120 188 68 116.49 1.37 182 121 124 3 367.06 1.11 183 121 125 4 365.62 0.77 184 121 150 29 296.87 0.89 185 122 125 3 366.96 1.06 186 122 126 4 365.62 0.77 187 123 126 3 365.99 0.58 188 123 127 4 365.04 1.05 189 123 146 23 313.53 0.89 190 123 147 24 313.48 0.91 191 123 149 26 295.70 2.04 192 124 127 3 365.28 0.91 193 124 128 4 364.62 0.89 194 124 149 25 304.54 2.24 195 124 150 26 293.00 1.01 196 124 151 27 292.71 0.94 197 125 128 3 368.04 0.47 198 125 129 4 362.49 1.52 199 126 129 3 366.28 1.35 200 126 130 4 353.60 5.96 201 126 146 20 313.55 0.89 202 127 130 3 367.45 0.96 203 127 131 4 358.06 4.46 204 127 149 22 299.88 0.07 205 127 159 32 222.07 0.57 206 128 131 3 367.17 1.11 207 128 132 4 367.06 1.17 208 129 132 3 367.06 1.16 209 129 133 4 365.87 0.57 210 130 133 3 365.87 0.57 211 130 138 8 314.12 0.88 212 130 141 11 314.07 0.88 213 130 144 14 313.77 0.89 214 130 159 29 222.06 0.57 215 130 162 32 221.89 0.58 216 131 138 7 314.42 0.78 217 131 160 29 222.02 0.58 218 131 161 30 221.97 0.58 219 133 137 4 365.48 0.78 220 133 138 5 339.39 12.26 221 133 141 8 314.50 0.75 222 134 137 3 382.97 0.54 223 134 138 4 345.88 10.53 224 135 138 3 377.87 3.08 225 135 139 4 343.35 11.80 226 136 139 3 373.61 1.87 227 136 140 4 349.56 8.71 228 137 140 3 378.10 3.20 229 137 141 4 361.57 4.23 230 138 141 3 381.83 4.17 231 138 161 23 221.96 0.59 232 138 162 24 221.75 0.62 233 139 166 27 220.44 0.73 234 141 144 3 414.05 0.24 235 141 162 21 221.79 0.62 236 141 166 25 220.32 0.74 237 142 166 24 220.37 0.77 238 142 206 64 83.44 0.18 239 142 207 65 82.72 0.53 240 142 210 68 77.25 0.66 241 143 162 19 221.95 0.61 242 143 166 23 220.31 0.74 243 143 202 59 107.96 0.97 244 143 203 60 106.64 0.40 245 143 206 63 84.53 0.41 246 144 159 15 222.06 0.57 247 144 162 18 221.93 0.61 248 144 166 22 220.40 0.77 249 144 167 23 220.27 0.76 250 144 168 24 220.27 0.76 251 144 202 58 108.31 1.13 252 144 203 59 107.50 0.83 253 145 168 23 220.24 0.76 254 145 170 25 220.18 0.77 255 145 199 54 108.44 1.13 256 145 202 57 108.39 1.09 257 145 203 58 107.95 0.97 258 146 149 3 373.54 1.36 259 146 159 13 222.09 0.58 260 146 167 21 220.41 0.78 261 146 168 22 220.28 0.76 262 146 169 23 220.22 0.75 263 146 170 24 220.21 0.75 264 147 170 23 220.13 0.78 265 147 191 44 112.91 0.12 266 147 194 47 112.54 0.01 267 147 195 48 112.57 0.06 268 147 199 52 112.45 0.01 269 148 170 22 220.22 0.74 270 148 171 23 220.11 0.79 271 148 175 27 220.00 0.83 272 148 177 29 219.94 0.86 273 148 178 30 219.81 0.89 274 148 188 40 116.17 1.49 275 148 191 43 115.45 1.36 276 149 152 3 368.32 1.97 277 149 155 6 233.41 1.56 278 149 158 9 222.33 0.51 279 149 159 10 222.31 0.55 280 149 169 20 220.31 0.78 281 149 171 22 220.18 0.77 282 149 177 28 220.02 0.83 283 149 178 29 219.28 0.57 284 150 177 27 219.87 0.90 285 150 182 32 164.93 2.71 286 151 154 3 357.69 6.22 287 151 155 4 300.44 31.96 288 152 155 3 372.01 2.00 289 152 156 4 294.56 34.90 290 152 157 5 222.53 0.60 291 152 169 17 220.61 0.83 292 152 171 19 220.40 0.80 293 152 178 26 219.87 0.90 294 153 156 3 313.24 25.57 295 153 178 25 220.19 0.74 296 153 179 26 219.79 0.93 297 153 180 27 215.97 0.96 298 154 180 26 215.45 0.70 299 155 158 3 368.73 0.73 300 155 160 5 223.30 0.70 301 157 169 12 220.61 0.83 302 158 162 4 370.49 1.48 303 158 163 5 248.26 4.13 304 158 164 6 222.11 0.70 305 159 162 3 372.27 0.58 306 159 167 8 220.62 0.83 307 162 166 4 367.31 0.04 308 162 167 5 291.97 13.05 309 163 166 3 378.12 1.11 310 163 167 4 356.20 5.59 311 164 167 3 362.37 8.67 312 165 202 37 108.60 1.04 313 165 206 41 106.27 0.62 314 166 202 36 108.56 1.03 315 167 202 35 108.56 1.04 316 168 202 34 108.56 1.04 317 170 191 21 115.43 1.38 318 170 194 24 112.79 0.12 319 170 198 28 112.53 0.01 320 170 199 29 112.50 0.02 321 171 191 20 116.05 1.47 322 172 187 15 122.11 0.25 323 172 190 18 117.59 1.93 324 172 191 19 116.15 1.48 325 173 187 14 133.69 1.39 326 174 185 11 151.81 1.33 327 174 187 13 134.07 1.19 328 175 187 12 128.91 2.37 329 175 188 13 124.39 0.42 330 175 191 16 122.95 0.60 331 176 181 5 476.40 6.82 332 176 183 7 290.98 22.82 333 176 185 9 152.12 1.49 334 177 181 4 401.45 0.78 335 177 182 5 371.93 2.79 336 177 183 6 290.98 22.82 337 177 188 11 128.08 1.96 338 184 188 4 362.51 5.24 339 184 189 5 375.09 1.04 340 185 188 3 379.47 1.13 341 185 189 4 384.23 1.25 342 186 189 3 387.88 0.58 343 187 190 3 388.25 0.39 344 187 191 4 388.25 0.39 345 188 191 3 420.70 1.18 346 190 193 3 446.34 5.25 347 191 194 3 374.94 3.28 348 191 195 4 352.86 6.96 349 192 195 3 363.70 5.74 350 192 196 4 333.29 2.80 351 193 196 3 348.69 1.77 352 193 197 4 333.00 2.94 353 193 198 5 317.29 0.15 354 194 197 3 376.71 6.69 355 194 198 4 317.26 0.17 356 194 199 5 260.21 2.02 357 194 200 6 261.33 1.45 358 195 199 4 260.22 2.02 359 195 200 5 260.22 2.02 360 196 200 4 351.83 9.12 361 197 200 3 377.51 1.84 362 197 201 4 351.81 9.12 363 198 201 3 369.22 0.42 364 198 202 4 351.82 9.12 365 199 202 3 370.89 1.27 366 199 203 4 336.83 1.09 367 200 203 3 349.93 2.60 368 200 204 4 326.95 1.76 369 201 204 3 366.81 5.84 370 201 205 4 337.74 0.67 371 202 205 3 353.31 7.12 372 202 206 4 337.74 0.67 373 203 206 3 364.70 3.46 374 203 207 4 329.35 2.93 375 204 207 3 363.10 2.66 376 204 208 4 329.35 2.93 377 205 208 3 352.68 7.86 378 205 209 4 329.35 2.93 379 206 209 3 373.58 2.79 380 206 210 4 373.23 2.62 381 207 210 3 381.34 3.00 382 207 211 4 325.18 0.92 383 208 211 3 373.22 2.62 384 208 212 4 278.24 22.37