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 64.81 0.33 2 18 46 28 64.78 0.31 3 18 47 29 64.73 0.33 4 18 48 30 54.61 0.43 5 18 49 31 58.25 1.36 6 18 53 35 52.48 0.45 7 19 46 27 64.86 0.35 8 19 47 28 64.86 0.35 9 20 47 27 65.52 0.15 10 20 48 28 64.88 0.35 11 20 56 36 64.86 0.35 12 20 60 40 64.86 0.35 13 20 65 45 64.79 0.30 14 20 70 50 64.78 0.31 15 20 71 51 64.83 0.33 16 20 72 52 64.87 0.35 17 21 24 3 354.06 6.82 18 21 25 4 288.88 24.98 19 21 47 26 65.86 0.09 20 21 71 50 65.52 0.15 21 22 25 3 340.50 0.08 22 22 26 4 279.29 29.65 23 22 69 47 65.80 0.09 24 22 70 48 65.81 0.07 25 22 71 49 65.86 0.09 26 23 26 3 351.78 6.20 27 23 35 12 66.02 0.15 28 23 37 14 66.57 0.38 29 23 69 46 66.02 0.15 30 23 71 48 66.06 0.14 31 23 101 78 70.22 0.10 32 23 104 81 70.28 0.10 33 23 105 82 68.97 0.12 34 23 108 85 70.28 0.10 35 24 71 47 68.75 0.81 36 24 101 77 69.95 0.23 37 24 108 84 71.75 0.19 38 26 69 43 69.39 0.48 39 26 108 82 139.22 2.18 40 27 30 3 379.68 0.85 41 27 31 4 334.45 2.65 42 27 69 42 528.67 5.77 43 28 31 3 371.28 5.05 44 28 108 80 201.63 10.68 45 32 112 80 454.64 2.72 46 33 112 79 454.63 2.72 47 33 113 80 454.62 2.71 48 33 211 178 39.58 0.33 49 34 113 79 454.64 2.71 50 34 115 81 454.62 2.71 51 34 207 173 80.20 0.64 52 34 211 177 38.52 0.21 53 35 112 77 530.75 4.21 54 35 113 78 458.20 2.56 55 35 114 79 454.64 2.71 56 35 115 80 454.64 2.71 57 36 115 79 454.65 2.71 58 36 116 80 454.64 2.71 59 36 117 81 454.63 2.71 60 36 203 167 104.51 0.33 61 37 115 78 457.24 2.48 62 37 116 79 454.64 2.71 63 37 117 80 454.64 2.71 64 38 117 79 454.64 2.71 65 38 118 80 454.63 2.71 66 38 119 81 454.63 2.71 67 38 147 109 311.39 0.90 68 39 117 78 455.64 3.12 69 39 118 79 454.63 2.71 70 39 119 80 454.63 2.71 71 39 122 83 364.24 1.68 72 39 125 86 361.61 3.00 73 40 119 79 454.64 2.71 74 40 122 82 364.35 1.74 75 41 119 78 454.69 2.73 76 41 120 79 454.64 2.71 77 42 121 79 454.63 2.72 78 44 119 75 455.70 3.12 79 51 119 68 454.62 2.71 80 51 147 96 309.76 0.55 81 51 191 140 112.86 0.59 82 51 192 141 112.48 0.58 83 51 195 144 108.11 0.67 84 54 195 141 108.12 0.66 85 54 196 142 108.08 0.68 86 55 147 92 309.73 0.54 87 55 195 140 108.09 0.68 88 55 200 145 107.95 0.72 89 55 203 148 106.98 0.59 90 58 196 138 108.08 0.69 91 58 200 142 107.95 0.73 92 58 204 146 104.52 0.33 93 59 115 56 455.51 3.07 94 59 203 144 104.53 0.33 95 59 204 145 103.81 0.64 96 62 204 142 103.83 0.64 97 62 208 146 84.45 1.49 98 63 204 141 103.81 0.64 99 63 207 144 84.82 1.31 100 73 125 52 361.61 3.00 101 77 121 44 454.60 2.73 102 77 122 45 449.99 3.51 103 77 125 48 362.57 2.56 104 79 121 42 454.60 2.73 105 80 121 41 455.61 3.17 106 83 121 38 455.62 3.18 107 84 121 37 455.76 3.10 108 84 150 66 309.39 0.48 109 84 182 98 174.03 3.09 110 85 182 97 179.62 0.30 111 87 151 64 305.42 1.03 112 88 124 36 433.61 7.19 113 88 128 40 364.14 1.79 114 88 131 43 362.07 2.82 115 88 132 44 361.97 2.78 116 88 151 63 300.12 1.11 117 89 121 32 454.67 2.73 118 89 124 35 387.07 1.84 119 89 151 62 300.25 1.05 120 90 121 31 454.63 2.73 121 90 125 35 364.19 1.81 122 94 125 31 361.65 3.03 123 95 125 30 361.66 3.03 124 95 128 33 359.29 2.17 125 95 129 34 339.48 0.80 126 95 132 37 332.72 0.34 127 98 125 27 361.63 3.02 128 98 126 28 361.53 2.99 129 98 129 31 334.22 1.08 130 99 129 30 334.21 1.08 131 99 132 33 330.89 0.42 132 99 133 34 315.58 2.35 133 102 114 12 524.86 4.73 134 102 116 14 454.69 2.73 135 102 129 27 334.05 1.17 136 102 130 28 332.56 0.44 137 102 133 31 312.34 0.73 138 102 137 35 312.13 0.76 139 102 141 39 311.95 0.82 140 103 137 34 312.12 0.76 141 105 114 9 462.86 5.16 142 106 137 31 312.11 0.75 143 106 140 34 311.97 0.82 144 109 112 3 454.62 2.71 145 110 140 30 311.91 0.80 146 111 211 100 41.29 0.50 147 112 211 99 39.63 0.33 148 113 142 29 311.80 0.83 149 113 207 94 80.20 0.63 150 113 210 97 42.51 0.10 151 113 211 98 39.61 0.31 152 114 137 23 312.14 0.76 153 114 140 26 311.95 0.82 154 114 141 27 311.84 0.82 155 114 142 28 311.84 0.83 156 115 141 26 311.92 0.82 157 115 142 27 311.88 0.84 158 115 143 28 311.68 0.90 159 115 203 88 104.65 0.40 160 115 207 92 84.98 0.63 161 116 130 14 332.51 0.46 162 116 141 25 311.94 0.82 163 116 143 27 311.87 0.83 164 116 144 28 311.45 0.88 165 116 145 29 311.38 0.85 166 116 203 87 105.97 0.46 167 117 144 27 311.72 0.89 168 117 145 28 311.36 0.85 169 118 122 4 364.37 1.76 170 118 123 5 364.08 1.75 171 118 126 8 361.12 2.81 172 118 145 27 311.75 0.87 173 118 146 28 311.32 0.86 174 118 147 29 309.95 0.46 175 119 122 3 365.87 1.03 176 119 123 4 364.42 1.71 177 119 147 28 309.80 0.52 178 119 188 69 115.58 0.23 179 119 189 70 115.42 0.28 180 119 191 72 112.88 0.59 181 120 123 3 372.70 0.85 182 120 124 4 365.52 1.20 183 120 147 27 311.64 0.89 184 120 148 28 309.74 0.51 185 120 150 30 304.78 1.14 186 120 188 68 115.58 0.23 187 121 124 3 369.37 1.14 188 121 125 4 365.03 1.44 189 121 150 29 304.78 1.14 190 122 125 3 369.32 1.12 191 122 126 4 364.93 1.40 192 123 126 3 370.54 3.70 193 123 127 4 365.62 1.04 194 123 146 23 311.69 0.89 195 123 147 24 311.64 0.89 196 123 149 26 304.79 1.14 197 124 127 3 370.87 3.54 198 124 128 4 365.64 1.02 199 124 149 25 305.21 0.93 200 124 150 26 300.33 1.01 201 124 151 27 297.78 1.28 202 125 128 3 375.05 1.45 203 125 129 4 364.56 0.48 204 126 129 3 366.42 1.28 205 126 130 4 358.56 2.52 206 126 146 20 311.69 0.91 207 127 130 3 377.03 0.45 208 127 131 4 358.68 2.58 209 127 149 22 305.22 0.93 210 127 159 32 218.90 1.03 211 128 131 3 363.18 2.85 212 128 132 4 356.51 3.66 213 129 132 3 369.09 2.69 214 129 133 4 356.45 3.64 215 130 133 3 364.33 0.31 216 130 138 8 312.19 0.77 217 130 141 11 312.16 0.79 218 130 144 14 311.96 0.83 219 130 159 29 218.89 1.03 220 130 162 32 218.36 1.19 221 131 138 7 313.37 0.55 222 131 160 29 218.82 1.02 223 131 161 30 218.70 1.05 224 133 137 4 351.41 7.02 225 133 138 5 315.60 0.18 226 133 141 8 314.67 0.08 227 134 137 3 381.97 0.04 228 134 138 4 350.44 6.49 229 135 138 3 369.31 1.94 230 135 139 4 351.36 6.03 231 136 139 3 380.61 3.71 232 136 140 4 369.31 1.95 233 137 140 3 377.86 2.33 234 137 141 4 377.86 2.33 235 138 141 3 380.83 3.67 236 138 161 23 218.35 1.22 237 138 162 24 218.16 1.17 238 139 166 27 217.32 0.80 239 141 144 3 414.95 0.21 240 141 162 21 218.19 1.19 241 141 166 25 217.13 0.83 242 142 166 24 217.12 0.82 243 142 206 64 87.17 1.18 244 142 207 65 85.02 0.64 245 142 210 68 75.95 0.70 246 143 162 19 218.33 1.21 247 143 166 23 217.11 0.82 248 143 202 59 107.84 0.67 249 143 203 60 106.32 0.59 250 143 206 63 87.73 1.46 251 144 159 15 218.87 1.04 252 144 162 18 218.26 1.22 253 144 166 22 217.15 0.83 254 144 167 23 217.02 0.86 255 144 168 24 217.00 0.87 256 144 202 58 107.99 0.73 257 144 203 59 106.95 0.62 258 145 168 23 216.99 0.86 259 145 170 25 216.86 0.82 260 145 199 54 108.12 0.66 261 145 202 57 108.10 0.68 262 145 203 58 107.94 0.72 263 146 149 3 372.54 0.86 264 146 159 13 218.91 1.04 265 146 167 21 217.15 0.83 266 146 168 22 217.05 0.85 267 146 169 23 216.91 0.84 268 146 170 24 216.71 0.89 269 147 170 23 216.34 0.89 270 147 191 44 112.88 0.59 271 147 194 47 112.56 0.65 272 147 195 48 112.58 0.64 273 147 199 52 112.35 0.62 274 148 170 22 216.96 0.86 275 148 171 23 216.34 0.90 276 148 175 27 216.31 0.88 277 148 177 29 216.24 0.89 278 148 178 30 216.03 0.92 279 148 188 40 115.48 0.28 280 148 191 43 114.65 0.29 281 149 152 3 359.69 5.29 282 149 155 6 290.94 14.12 283 149 157 8 219.41 1.22 284 149 158 9 219.27 1.15 285 149 159 10 219.18 1.11 286 149 169 20 217.03 0.85 287 149 171 22 216.72 0.89 288 149 178 29 215.93 0.97 289 150 154 4 382.62 2.52 290 150 177 27 216.01 0.91 291 150 182 32 179.60 0.29 292 151 154 3 372.15 1.02 293 151 155 4 349.37 5.18 294 152 155 3 376.80 0.39 295 152 156 4 339.48 10.12 296 152 157 5 219.44 1.25 297 152 169 17 217.19 0.83 298 152 171 19 217.03 0.89 299 152 178 26 215.94 0.97 300 153 156 3 349.37 5.17 301 153 178 25 216.97 0.88 302 153 179 26 215.93 0.97 303 153 180 27 212.38 0.17 304 154 180 26 211.86 0.45 305 155 158 3 367.73 1.23 306 155 160 5 229.11 5.87 307 157 169 12 217.26 0.80 308 158 162 4 371.00 1.22 309 158 163 5 247.70 3.42 310 158 164 6 218.56 1.08 311 159 162 3 372.59 0.10 312 159 167 8 217.37 0.81 313 162 166 4 372.47 3.62 314 162 167 5 317.35 0.36 315 163 166 3 378.86 0.42 316 163 167 4 349.55 7.76 317 164 167 3 374.16 2.77 318 165 202 37 108.20 0.69 319 165 206 41 106.34 0.60 320 166 202 36 108.17 0.69 321 166 210 44 87.72 1.46 322 167 202 35 108.18 0.68 323 168 202 34 108.19 0.69 324 170 191 21 114.70 0.28 325 170 194 24 112.52 0.68 326 170 198 28 112.49 0.69 327 170 199 29 112.46 0.67 328 171 191 20 116.32 0.20 329 172 187 15 121.16 0.67 330 172 190 18 119.26 1.09 331 172 191 19 116.89 0.42 332 173 187 14 133.51 0.29 333 174 185 11 155.73 0.06 334 174 187 13 133.51 0.29 335 175 187 12 133.51 0.29 336 175 188 13 133.51 0.29 337 175 191 16 131.34 0.14 338 176 181 5 445.78 1.12 339 176 183 7 371.61 5.04 340 176 185 9 193.78 18.96 341 177 181 4 402.69 0.85 342 177 182 5 380.31 0.69 343 177 183 6 343.10 9.21 344 177 188 11 132.56 0.77 345 184 188 4 346.84 1.71 346 184 189 5 357.19 3.47 347 185 188 3 387.25 0.89 348 186 189 3 387.26 0.89 349 186 190 4 382.10 3.47 350 187 190 3 387.25 0.90 351 187 191 4 387.25 0.90 352 188 191 3 419.70 0.68 353 190 193 3 438.55 2.36 354 191 194 3 384.80 1.66 355 191 195 4 332.11 2.50 356 192 195 3 378.94 4.58 357 192 196 4 332.12 2.50 358 193 196 3 357.47 9.00 359 193 197 4 332.12 2.50 360 193 198 5 332.11 2.50 361 194 197 3 366.42 10.84 362 194 198 4 321.62 0.37 363 194 199 5 321.62 0.36 364 194 200 6 321.62 0.37 365 195 199 4 321.61 0.36 366 195 200 5 321.58 0.36 367 196 200 4 340.79 2.77 368 197 200 3 376.70 1.45 369 197 201 4 332.04 2.56 370 198 201 3 337.11 4.62 371 198 202 4 332.44 2.31 372 199 202 3 353.04 0.04 373 199 203 4 345.97 5.66 374 200 203 3 369.85 0.73 375 200 204 4 324.77 1.54 376 201 204 3 377.26 0.62 377 201 205 4 329.05 3.68 378 202 205 3 371.42 0.10 379 202 206 4 337.40 0.50 380 203 206 3 363.70 3.97 381 203 207 4 336.81 0.80 382 204 207 3 360.45 3.15 383 204 208 4 336.80 0.80 384 205 208 3 355.81 5.47 385 205 209 4 350.98 7.88 386 206 209 3 350.84 13.17 387 206 210 4 364.07 6.55 388 207 210 3 381.45 3.05 389 207 211 4 318.67 1.36 390 208 211 3 363.73 6.37 391 208 212 4 288.21 14.10