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 61.14 0.75 2 18 46 28 61.14 0.76 3 18 47 29 61.23 0.70 4 18 48 30 49.49 1.95 5 18 49 31 56.42 0.48 6 18 53 35 41.24 0.01 7 19 46 27 61.95 0.65 8 19 47 28 61.26 0.70 9 20 47 27 64.27 0.06 10 20 48 28 62.16 0.56 11 20 60 40 61.29 0.68 12 20 70 50 61.26 0.67 13 20 71 51 62.01 0.63 14 20 72 52 62.55 0.74 15 21 24 3 371.15 3.32 16 21 25 4 284.26 27.14 17 21 47 26 64.86 0.30 18 21 71 50 63.91 0.12 19 22 25 3 359.49 9.15 20 22 26 4 223.56 1.77 21 22 69 47 64.75 0.29 22 22 70 48 64.78 0.31 23 22 71 49 64.88 0.33 24 23 26 3 354.37 7.92 25 23 35 12 64.89 0.33 26 23 37 14 65.39 0.09 27 23 69 46 64.89 0.32 28 23 71 48 65.39 0.09 29 23 101 78 68.22 1.09 30 23 104 81 68.36 1.08 31 23 105 82 67.59 0.80 32 23 108 85 68.31 1.05 33 24 71 47 66.45 0.61 34 24 101 77 68.36 1.08 35 24 108 84 125.17 0.44 36 26 69 43 68.00 1.17 37 26 108 82 135.18 4.59 38 27 30 3 371.29 5.05 39 27 31 4 359.54 0.83 40 27 69 42 534.13 4.11 41 28 31 3 364.21 0.37 42 28 108 80 169.03 5.62 43 32 112 80 459.40 0.68 44 33 112 79 459.40 0.68 45 33 113 80 459.40 0.68 46 33 211 178 39.58 0.33 47 34 113 79 459.40 0.68 48 34 115 81 459.38 0.67 49 34 207 173 80.28 0.55 50 34 211 177 39.55 0.31 51 35 112 77 527.63 2.65 52 35 113 78 461.99 0.67 53 35 114 79 459.40 0.67 54 35 115 80 459.39 0.68 55 36 115 79 459.40 0.67 56 36 116 80 459.39 0.68 57 36 117 81 459.39 0.68 58 36 203 167 104.11 0.49 59 37 115 78 460.49 0.85 60 37 116 79 459.41 0.68 61 37 117 80 459.41 0.68 62 38 117 79 459.41 0.68 63 38 118 80 459.39 0.68 64 38 119 81 459.40 0.68 65 39 117 78 460.28 0.81 66 39 118 79 459.39 0.68 67 39 119 80 459.39 0.68 68 39 122 83 361.45 0.29 69 39 125 86 358.82 0.93 70 40 119 79 459.41 0.67 71 40 122 82 362.90 0.33 72 41 119 78 459.48 0.68 73 41 120 79 459.41 0.67 74 42 121 79 459.43 0.67 75 44 119 75 460.41 0.88 76 51 119 68 459.37 0.68 77 51 147 96 309.14 0.32 78 51 191 140 112.44 0.63 79 51 192 141 111.92 0.60 80 51 195 144 108.78 1.01 81 54 195 141 109.81 0.48 82 54 196 142 108.75 1.01 83 55 147 92 309.12 0.33 84 55 195 140 108.78 0.98 85 55 200 145 108.36 0.93 86 55 203 148 107.58 1.13 87 58 196 138 108.97 0.87 88 58 200 142 108.28 0.89 89 58 204 146 104.09 0.51 90 59 115 56 460.14 0.74 91 59 203 144 104.47 0.30 92 59 204 145 103.32 0.27 93 62 204 142 103.62 0.35 94 62 208 146 84.45 1.50 95 63 204 141 103.23 0.31 96 63 207 144 84.48 1.49 97 73 125 52 358.82 0.93 98 77 121 44 459.38 0.70 99 77 122 45 452.23 2.39 100 77 125 48 358.85 0.93 101 79 121 42 459.41 0.69 102 80 121 41 459.56 0.68 103 83 121 38 460.08 0.90 104 84 121 37 460.08 0.90 105 84 182 98 152.43 3.94 106 85 182 97 173.84 6.12 107 87 151 64 304.37 1.55 108 88 124 36 439.13 5.96 109 88 128 40 358.91 0.93 110 88 131 43 358.78 0.93 111 88 132 44 358.60 0.97 112 88 151 63 293.14 1.06 113 89 121 32 459.45 0.67 114 89 124 35 405.30 10.96 115 89 151 62 293.13 1.09 116 90 121 31 459.44 0.67 117 90 125 35 361.54 0.28 118 94 125 31 359.13 0.80 119 95 125 30 358.85 0.94 120 95 128 33 357.62 0.83 121 95 129 34 339.48 0.80 122 95 132 37 329.04 1.25 123 98 125 27 358.83 0.93 124 98 126 28 358.57 0.86 125 98 129 31 329.25 1.26 126 99 129 30 329.20 1.24 127 99 132 33 327.75 1.16 128 99 133 34 311.95 0.14 129 102 114 12 523.28 3.12 130 102 116 14 459.47 0.68 131 102 129 27 333.99 1.15 132 102 130 28 329.18 1.24 133 102 133 31 311.05 0.31 134 102 137 35 310.93 0.32 135 102 141 39 310.81 0.29 136 103 137 34 310.93 0.32 137 105 114 9 507.44 17.10 138 106 137 31 310.88 0.30 139 106 140 34 310.82 0.28 140 109 112 3 459.39 0.68 141 110 140 30 310.80 0.29 142 111 211 100 39.63 0.33 143 112 211 99 39.63 0.33 144 113 140 27 310.80 0.29 145 113 142 29 310.47 0.28 146 113 207 94 80.29 0.55 147 113 210 97 41.54 0.38 148 113 211 98 39.59 0.33 149 114 137 23 310.94 0.30 150 114 140 26 310.81 0.28 151 114 141 27 310.75 0.28 152 114 142 28 310.69 0.29 153 115 141 26 310.80 0.29 154 115 142 27 310.74 0.29 155 115 143 28 310.31 0.20 156 115 203 88 104.28 0.58 157 115 207 92 82.39 0.49 158 116 130 14 329.14 1.23 159 116 141 25 310.81 0.28 160 116 143 27 310.69 0.29 161 116 144 28 310.07 0.20 162 116 145 29 310.03 0.21 163 116 203 87 105.76 0.31 164 117 144 27 310.38 0.24 165 117 145 28 310.07 0.24 166 118 122 4 361.60 0.32 167 118 123 5 359.72 1.14 168 118 126 8 358.51 0.90 169 118 145 27 310.36 0.25 170 118 146 28 310.03 0.21 171 118 147 29 309.28 0.40 172 119 122 3 366.97 1.44 173 119 123 4 361.62 0.31 174 119 147 28 309.14 0.33 175 119 188 69 115.29 0.38 176 119 189 70 115.25 0.36 177 119 191 72 112.46 0.64 178 120 123 3 372.51 1.79 179 120 124 4 363.48 0.11 180 120 147 27 310.23 0.28 181 120 148 28 309.14 0.33 182 120 150 30 302.76 2.44 183 120 188 68 115.30 0.37 184 121 124 3 369.46 1.09 185 121 125 4 363.00 0.35 186 121 150 29 297.93 0.07 187 122 125 3 369.31 2.10 188 122 126 4 362.23 0.61 189 123 126 3 365.16 1.12 190 123 127 4 362.23 0.61 191 123 146 23 310.30 0.28 192 123 147 24 310.21 0.28 193 123 149 26 295.50 1.15 194 124 127 3 361.81 0.41 195 124 128 4 361.62 0.33 196 124 149 25 303.51 1.75 197 124 150 26 293.13 1.07 198 124 151 27 292.67 0.88 199 125 128 3 372.56 1.79 200 125 129 4 360.48 0.90 201 126 129 3 372.32 4.37 202 126 130 4 355.31 3.48 203 126 146 20 310.32 0.27 204 127 130 3 372.45 4.55 205 127 131 4 355.31 3.48 206 127 149 22 298.91 0.56 207 127 159 32 221.74 1.85 208 128 131 3 366.53 1.17 209 128 132 4 355.28 3.46 210 129 132 3 366.53 1.17 211 129 133 4 348.81 6.66 212 130 133 3 364.82 0.07 213 130 138 8 310.98 0.31 214 130 141 11 310.98 0.32 215 130 144 14 310.82 0.30 216 130 159 29 221.72 1.85 217 130 162 32 221.61 1.84 218 131 138 7 312.13 0.07 219 131 160 29 221.69 1.86 220 131 161 30 221.65 1.84 221 133 137 4 365.41 0.77 222 133 138 5 338.45 12.73 223 133 141 8 312.16 0.07 224 134 137 3 381.97 0.03 225 134 138 4 365.64 0.70 226 135 138 3 367.99 1.86 227 135 139 4 366.49 1.31 228 136 139 3 381.97 3.02 229 136 140 4 368.74 2.23 230 137 140 3 380.69 3.74 231 137 141 4 377.86 2.33 232 138 141 3 380.69 3.74 233 138 161 23 221.63 1.85 234 138 162 24 221.53 1.89 235 139 166 27 220.41 1.68 236 141 144 3 411.14 0.67 237 141 162 21 221.52 1.89 238 141 166 25 220.31 1.70 239 142 166 24 220.28 1.71 240 142 206 64 84.52 0.07 241 142 207 65 82.52 0.43 242 142 210 68 79.28 0.97 243 143 162 19 221.62 1.85 244 143 166 23 220.28 1.71 245 143 202 59 108.28 0.89 246 143 203 60 106.45 0.54 247 143 206 63 86.70 1.02 248 144 159 15 221.74 1.85 249 144 162 18 221.61 1.85 250 144 166 22 220.36 1.72 251 144 167 23 220.27 1.71 252 144 168 24 220.25 1.71 253 144 202 58 108.56 1.01 254 144 203 59 107.77 1.03 255 145 168 23 220.22 1.70 256 145 170 25 219.96 1.74 257 145 199 54 108.75 0.97 258 145 202 57 108.68 0.96 259 145 203 58 108.53 1.02 260 146 149 3 372.54 0.86 261 146 159 13 221.78 1.83 262 146 167 21 220.38 1.71 263 146 168 22 220.28 1.72 264 146 169 23 220.17 1.68 265 146 170 24 219.96 1.74 266 147 170 23 219.93 1.75 267 147 191 44 112.49 0.66 268 147 194 47 111.90 0.61 269 147 195 48 111.92 0.60 270 147 199 52 111.84 0.60 271 148 170 22 220.22 1.70 272 148 171 23 219.92 1.75 273 148 175 27 218.84 1.19 274 148 177 29 217.96 1.65 275 148 178 30 217.21 1.41 276 148 188 40 115.30 0.38 277 148 191 43 114.65 0.33 278 149 152 3 369.78 0.24 279 149 155 6 313.53 25.42 280 149 158 9 221.88 1.83 281 149 159 10 221.93 1.85 282 149 169 20 220.34 1.69 283 149 171 22 220.13 1.66 284 149 177 28 217.95 1.65 285 149 178 29 217.06 1.49 286 150 154 4 382.61 2.52 287 150 177 27 217.39 1.39 288 151 154 3 372.16 1.01 289 151 155 4 318.50 25.80 290 152 155 3 372.41 1.81 291 152 156 4 309.67 27.36 292 152 157 5 222.38 1.76 293 152 169 17 220.53 1.71 294 152 171 19 220.34 1.70 295 152 178 26 217.11 1.46 296 153 156 3 362.13 1.11 297 153 178 25 219.93 1.76 298 153 179 26 218.79 2.31 299 153 180 27 216.98 1.50 300 154 180 26 215.91 0.97 301 155 158 3 369.32 2.02 302 155 160 5 222.52 1.68 303 157 169 12 220.53 1.71 304 158 162 4 361.30 6.07 305 158 163 5 241.08 6.74 306 158 164 6 222.13 1.75 307 159 162 3 371.00 1.22 308 159 167 8 221.25 1.35 309 162 166 4 366.31 0.54 310 162 167 5 336.53 11.50 311 163 166 3 377.12 1.61 312 163 167 4 366.23 0.58 313 164 167 3 368.00 0.30 314 165 202 37 108.73 0.95 315 165 206 41 106.53 0.49 316 166 202 36 108.72 0.96 317 167 202 35 108.73 0.96 318 168 202 34 108.73 0.96 319 170 191 21 114.69 0.34 320 170 194 24 111.86 0.59 321 170 198 28 111.84 0.60 322 170 199 29 111.86 0.61 323 171 191 20 116.36 0.17 324 172 187 15 121.45 0.29 325 172 190 18 119.80 0.51 326 172 191 19 116.75 0.01 327 172 194 22 115.18 0.41 328 173 187 14 127.05 2.94 329 174 185 11 146.65 2.66 330 174 187 13 127.88 2.52 331 175 187 12 126.52 2.82 332 175 188 13 126.89 3.02 333 175 191 16 126.35 2.74 334 176 181 5 472.75 2.61 335 176 183 7 336.41 1.49 336 176 185 9 153.22 0.62 337 177 181 4 402.79 0.90 338 177 182 5 370.93 2.29 339 177 183 6 336.41 1.49 340 177 188 11 126.34 2.74 341 184 188 4 362.44 1.38 342 184 189 5 362.46 1.39 343 185 188 3 387.61 0.71 344 186 189 3 386.88 1.07 345 186 190 4 386.87 1.08 346 187 190 3 387.25 0.89 347 187 191 4 387.25 0.89 348 188 191 3 419.70 0.68 349 190 193 3 431.19 1.32 350 191 194 3 380.39 0.55 351 191 195 4 369.18 1.20 352 192 195 3 373.38 0.90 353 192 196 4 351.49 7.65 354 193 196 3 358.37 6.61 355 193 197 4 326.50 2.90 356 193 198 5 326.20 3.04 357 194 197 3 381.50 3.30 358 194 198 4 324.66 2.30 359 194 199 5 322.10 3.44 360 194 200 6 324.49 2.25 361 195 199 4 316.62 0.70 362 195 200 5 319.00 0.49 363 196 200 4 368.23 0.09 364 197 200 3 376.70 1.45 365 197 201 4 350.84 8.77 366 198 201 3 368.22 0.09 367 198 202 4 350.84 8.77 368 199 202 3 369.91 0.76 369 199 203 4 352.70 7.84 370 200 203 3 360.76 3.81 371 200 204 4 329.05 3.68 372 201 204 3 374.86 1.82 373 201 205 4 349.43 11.10 374 202 205 3 371.43 0.10 375 202 206 4 339.84 1.72 376 203 206 3 363.71 3.97 377 203 207 4 339.23 2.02 378 204 207 3 360.46 3.15 379 204 208 4 350.99 7.89 380 205 208 3 355.83 5.48 381 205 209 4 351.00 7.90 382 206 209 3 372.58 2.29 383 206 210 4 372.58 2.29 384 207 210 3 381.45 3.05 385 207 211 4 349.50 8.64 386 208 211 3 371.41 2.53 387 208 212 4 290.86 15.23