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 63.18 0.58 2 18 46 28 63.18 0.58 3 18 47 29 63.17 0.58 4 18 48 30 56.06 0.29 5 18 49 31 57.04 1.61 6 18 53 35 50.52 1.43 7 19 46 27 63.80 0.40 8 19 47 28 63.19 0.59 9 20 47 27 65.23 0.21 10 20 48 28 64.32 0.45 11 20 56 36 63.30 0.52 12 20 60 40 63.47 0.43 13 20 65 45 65.18 0.13 14 20 70 50 63.18 0.58 15 20 71 51 63.90 0.24 16 20 72 52 64.45 0.39 17 21 24 3 362.79 2.46 18 21 25 4 331.29 3.73 19 21 47 26 65.75 0.14 20 21 71 50 65.20 0.21 21 22 25 3 354.18 6.76 22 22 26 4 284.36 27.19 23 22 69 47 65.48 0.07 24 22 70 48 65.53 0.07 25 22 71 49 65.78 0.12 26 23 26 3 354.47 7.87 27 23 35 12 65.84 0.14 28 23 37 14 65.87 0.14 29 23 69 46 65.80 0.13 30 23 71 48 65.86 0.14 31 23 101 78 70.21 0.11 32 23 104 81 70.68 0.30 33 23 105 82 69.57 0.18 34 23 108 85 70.71 0.23 35 24 71 47 68.87 0.75 36 24 101 77 70.75 0.26 37 24 104 80 71.39 0.01 38 24 108 84 99.08 13.49 39 26 69 43 70.91 0.28 40 26 108 82 176.47 26.16 41 27 30 3 367.44 3.12 42 27 31 4 345.60 7.79 43 27 69 42 536.03 1.95 44 28 31 3 373.98 3.71 45 28 108 80 183.90 22.55 46 32 112 80 459.39 0.68 47 33 112 79 459.39 0.68 48 33 113 80 459.39 0.68 49 33 211 178 35.60 0.53 50 34 113 79 459.39 0.68 51 34 115 81 459.38 0.67 52 34 207 173 80.78 0.30 53 34 211 177 35.63 0.56 54 35 112 77 495.83 13.21 55 35 113 78 461.98 0.61 56 35 114 79 459.39 0.68 57 35 115 80 459.39 0.68 58 36 115 79 459.39 0.68 59 36 116 80 459.39 0.68 60 36 117 81 459.39 0.68 61 36 203 167 104.55 0.27 62 37 115 78 460.50 0.84 63 37 116 79 459.39 0.67 64 37 117 80 459.39 0.68 65 38 117 79 459.40 0.68 66 38 118 80 459.39 0.68 67 38 119 81 459.39 0.68 68 38 147 109 315.10 0.42 69 39 117 78 460.31 0.83 70 39 118 79 459.39 0.68 71 39 119 80 459.39 0.68 72 39 122 83 365.25 0.48 73 39 125 86 363.43 1.36 74 40 119 79 459.41 0.68 75 40 122 82 365.48 0.33 76 41 119 78 459.48 0.69 77 41 120 79 459.40 0.68 78 42 121 79 459.41 0.68 79 44 119 75 460.25 0.96 80 51 119 68 459.25 0.73 81 51 147 96 313.66 0.07 82 51 191 140 112.50 0.67 83 51 192 141 112.19 0.73 84 51 195 144 108.78 1.01 85 54 195 141 109.37 1.31 86 54 196 142 108.76 1.01 87 55 147 92 313.61 0.10 88 55 195 140 108.77 1.02 89 55 200 145 108.28 0.89 90 55 203 148 107.38 1.15 91 58 196 138 108.73 1.02 92 58 200 142 108.26 0.88 93 58 204 146 104.33 0.17 94 59 115 56 459.91 0.91 95 59 203 144 104.54 0.26 96 59 204 145 104.10 0.12 97 62 204 142 103.63 0.35 98 62 208 146 84.44 1.50 99 63 204 141 103.62 0.35 100 63 207 144 85.92 0.76 101 73 125 52 363.43 1.36 102 77 121 44 459.38 0.70 103 77 122 45 456.17 0.36 104 77 125 48 365.08 0.63 105 79 121 42 459.44 0.68 106 80 121 41 460.07 0.96 107 83 121 38 460.04 0.95 108 84 121 37 460.00 0.93 109 84 182 98 150.23 4.33 110 85 182 97 158.75 1.43 111 87 151 64 308.89 3.53 112 88 124 36 434.20 8.43 113 88 128 40 364.60 0.90 114 88 131 43 363.43 1.40 115 88 132 44 363.37 1.42 116 88 151 63 296.95 0.84 117 89 121 32 459.46 0.67 118 89 124 35 391.15 2.31 119 89 151 62 297.15 0.74 120 90 121 31 459.42 0.68 121 90 125 35 366.19 0.55 122 94 125 31 363.55 1.38 123 95 125 30 363.55 1.38 124 95 128 33 360.67 0.70 125 95 129 34 338.78 0.45 126 95 132 37 332.29 0.48 127 98 125 27 363.44 1.35 128 98 126 28 363.35 1.39 129 98 129 31 332.56 0.43 130 99 129 30 334.17 0.38 131 99 132 33 327.75 1.16 132 99 133 34 316.69 0.35 133 102 114 12 529.06 2.65 134 102 116 14 459.48 0.69 135 102 129 27 334.00 1.15 136 102 130 28 332.54 0.45 137 102 133 31 316.69 0.35 138 102 137 35 316.52 0.29 139 102 141 39 316.25 0.26 140 103 137 34 316.51 0.28 141 105 114 9 499.75 16.43 142 106 137 31 316.49 0.28 143 106 140 34 316.25 0.26 144 109 112 3 459.39 0.68 145 110 140 30 316.22 0.27 146 111 211 100 39.62 0.32 147 113 142 29 316.01 0.27 148 113 207 94 80.78 0.29 149 113 210 97 42.49 0.10 150 113 211 98 39.59 0.33 151 114 137 23 316.50 0.28 152 114 140 26 316.27 0.24 153 114 141 27 316.18 0.27 154 114 142 28 316.17 0.27 155 115 141 26 316.24 0.26 156 115 142 27 316.21 0.25 157 115 143 28 315.74 0.23 158 115 203 88 104.74 0.35 159 115 207 92 84.81 0.71 160 116 130 14 332.50 0.46 161 116 141 25 316.28 0.24 162 116 143 27 316.18 0.27 163 116 144 28 315.40 0.21 164 116 145 29 315.39 0.21 165 116 203 87 105.93 0.38 166 117 144 27 316.12 0.26 167 117 145 28 315.39 0.21 168 118 122 4 365.33 0.51 169 118 123 5 365.14 0.49 170 118 126 8 363.19 1.44 171 118 145 27 316.07 0.24 172 118 146 28 315.23 0.13 173 118 147 29 313.73 0.07 174 119 122 3 369.39 1.05 175 119 123 4 365.81 0.72 176 119 147 28 313.67 0.06 177 119 188 69 119.19 1.57 178 119 189 70 119.12 1.58 179 119 191 72 112.52 0.67 180 120 123 3 377.58 0.74 181 120 124 4 374.46 2.30 182 120 147 27 315.80 0.26 183 120 148 28 313.67 0.06 184 120 150 30 302.75 2.44 185 120 188 68 119.29 1.62 186 121 124 3 369.58 1.13 187 121 125 4 369.55 1.14 188 121 150 29 297.85 1.08 189 122 125 3 369.54 1.14 190 122 126 4 366.18 0.54 191 123 126 3 372.52 2.71 192 123 127 4 366.10 0.50 193 123 146 23 315.83 0.24 194 123 147 24 315.75 0.23 195 123 149 26 297.87 1.09 196 124 127 3 372.51 2.71 197 124 128 4 365.23 0.69 198 124 149 25 303.56 1.73 199 124 150 26 293.17 1.05 200 124 151 27 292.94 1.05 201 125 128 3 372.24 2.85 202 125 129 4 365.11 0.69 203 126 129 3 367.74 0.62 204 126 130 4 365.59 0.42 205 126 146 20 316.03 0.26 206 127 130 3 370.44 2.85 207 127 131 4 360.39 2.18 208 127 149 22 298.96 0.59 209 127 159 32 226.02 0.14 210 128 131 3 368.69 0.09 211 128 132 4 365.97 0.61 212 129 132 3 369.60 2.43 213 129 133 4 366.06 0.66 214 130 133 3 364.14 4.07 215 130 138 8 316.60 0.30 216 130 141 11 316.53 0.27 217 130 144 14 316.25 0.26 218 130 159 29 226.02 0.14 219 130 162 32 225.81 0.20 220 131 138 7 316.87 0.35 221 131 160 29 225.99 0.14 222 131 161 30 225.94 0.17 223 133 137 4 339.37 0.89 224 133 138 5 316.88 0.36 225 133 141 8 316.88 0.36 226 134 137 3 381.97 0.03 227 134 138 4 348.42 12.38 228 135 138 3 355.39 8.90 229 135 139 4 320.71 1.49 230 136 140 4 348.54 9.20 231 137 140 3 377.86 2.33 232 137 141 4 376.62 2.94 233 138 141 3 383.71 2.23 234 138 161 23 225.64 0.10 235 138 162 24 225.46 0.08 236 139 166 27 224.89 0.32 237 141 144 3 413.50 0.52 238 141 162 21 225.48 0.09 239 141 166 25 224.83 0.29 240 142 166 24 224.81 0.29 241 142 206 64 86.14 1.30 242 142 207 65 84.82 0.72 243 142 210 68 77.34 0.88 244 143 162 19 225.61 0.10 245 143 166 23 224.81 0.29 246 143 202 59 108.54 1.02 247 143 203 60 106.03 0.42 248 143 206 63 86.70 1.03 249 144 159 15 225.97 0.16 250 144 162 18 225.63 0.10 251 144 166 22 224.94 0.24 252 144 167 23 224.75 0.30 253 144 168 24 224.72 0.29 254 144 202 58 108.56 1.01 255 144 203 59 107.44 0.86 256 145 168 23 224.69 0.28 257 145 170 25 224.43 0.24 258 145 199 54 108.78 0.98 259 145 202 57 108.56 1.02 260 145 203 58 108.53 1.02 261 146 149 3 372.54 0.86 262 146 159 13 226.01 0.14 263 146 167 21 224.97 0.23 264 146 168 22 224.76 0.30 265 146 169 23 224.63 0.28 266 146 170 24 224.38 0.22 267 147 170 23 224.18 0.18 268 147 191 44 112.58 0.70 269 147 194 47 112.28 0.78 270 147 195 48 112.27 0.78 271 147 199 52 112.07 0.72 272 148 170 22 224.66 0.29 273 148 171 23 224.19 0.18 274 148 175 27 224.47 0.32 275 148 177 29 223.98 0.10 276 148 178 30 223.63 0.10 277 148 188 40 119.20 1.57 278 148 191 43 117.77 1.25 279 149 152 3 369.01 0.14 280 149 155 6 289.63 14.77 281 149 157 8 226.68 0.24 282 149 158 9 226.47 0.13 283 149 159 10 226.44 0.14 284 149 169 20 224.75 0.25 285 149 171 22 224.52 0.29 286 149 177 28 223.98 0.10 287 149 178 29 222.86 0.29 288 150 154 4 382.61 2.52 289 150 177 27 223.77 0.03 290 151 154 3 372.16 1.01 291 151 155 4 353.89 7.45 292 152 155 3 376.80 0.39 293 152 156 4 343.97 12.41 294 152 157 5 228.53 1.16 295 152 169 17 225.03 0.24 296 152 171 19 224.86 0.28 297 152 178 26 223.34 0.06 298 153 156 3 366.58 1.10 299 153 178 25 224.36 0.15 300 153 179 26 223.33 0.06 301 153 180 27 222.81 0.30 302 154 180 26 222.88 0.26 303 155 158 3 362.24 3.98 304 155 160 5 228.50 1.17 305 157 169 12 224.99 0.24 306 158 162 4 361.30 6.07 307 158 163 5 237.16 2.42 308 158 164 6 225.84 0.01 309 159 162 3 370.75 0.83 310 159 167 8 225.05 0.26 311 162 166 4 376.81 1.45 312 162 167 5 251.58 4.04 313 163 166 3 377.26 1.23 314 163 167 4 345.05 11.18 315 164 167 3 374.16 2.77 316 165 202 37 108.77 0.97 317 165 206 41 106.54 0.50 318 166 202 36 108.71 0.96 319 167 202 35 108.73 0.96 320 168 202 34 108.76 0.96 321 170 191 21 116.50 0.61 322 170 194 24 112.29 0.79 323 170 198 28 112.13 0.74 324 170 199 29 112.12 0.75 325 171 191 20 119.20 1.48 326 172 187 15 120.53 1.52 327 172 190 18 120.29 1.63 328 172 191 19 119.42 1.50 329 173 187 14 129.16 0.51 330 174 185 11 146.65 2.66 331 174 187 13 129.33 0.58 332 175 187 12 129.16 0.51 333 175 188 13 120.91 1.46 334 175 191 16 122.32 0.75 335 176 181 5 428.31 3.08 336 176 183 7 350.75 5.69 337 176 185 9 146.65 2.69 338 177 181 4 398.84 1.08 339 177 182 5 372.52 1.49 340 177 183 6 350.75 5.69 341 177 188 11 121.92 1.11 342 184 188 4 337.87 0.56 343 184 189 5 350.21 0.02 344 185 188 3 383.92 1.12 345 186 189 3 387.25 0.89 346 186 190 4 386.88 1.07 347 187 190 3 387.26 0.89 348 187 191 4 388.55 0.24 349 188 191 3 419.70 0.68 350 190 193 3 438.55 2.36 351 191 194 3 380.39 0.55 352 191 195 4 352.00 7.39 353 192 195 3 373.39 1.81 354 192 196 4 352.00 7.39 355 193 196 3 361.31 7.19 356 193 197 4 342.06 2.43 357 193 198 5 336.16 0.52 358 194 197 3 375.71 6.19 359 194 198 4 336.15 0.52 360 194 199 5 319.02 1.04 361 194 200 6 319.03 1.05 362 195 199 4 319.02 1.04 363 195 200 5 319.02 1.04 364 196 200 4 350.15 8.96 365 197 200 3 376.51 1.34 366 197 201 4 326.16 2.16 367 198 201 3 339.30 3.52 368 198 202 4 333.75 1.64 369 199 202 3 369.89 0.77 370 199 203 4 335.83 0.59 371 200 203 3 362.12 4.58 372 200 204 4 334.86 0.77 373 201 204 3 377.26 0.62 374 201 205 4 337.41 0.51 375 202 205 3 371.42 0.10 376 202 206 4 339.83 1.72 377 203 206 3 363.70 3.97 378 203 207 4 355.86 6.29 379 204 207 3 367.32 0.57 380 204 208 4 355.85 6.30 381 205 208 3 357.36 7.04 382 205 209 4 355.84 6.30 383 206 209 3 372.88 2.15 384 206 210 4 372.81 2.19 385 207 210 3 381.45 3.05 386 207 211 4 334.19 2.09 387 208 211 3 363.73 6.37 388 208 212 4 234.48 0.10 389 208 213 5 190.95 21.86