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 46 28 96.52 19.20 2 18 47 29 96.59 19.23 3 18 48 30 93.66 20.29 4 18 49 31 94.65 19.79 5 18 53 35 86.76 23.80 6 19 46 27 97.25 19.46 7 19 47 28 98.08 19.98 8 19 48 29 96.59 19.23 9 20 47 27 103.44 22.08 10 20 48 28 103.00 22.29 11 20 60 40 112.06 26.94 12 20 65 45 112.97 26.51 13 20 70 50 103.30 22.59 14 20 71 51 103.28 22.43 15 20 72 52 103.26 22.40 16 21 24 3 370.29 3.96 17 21 25 4 248.91 2.43 18 21 47 26 110.10 25.01 19 21 71 50 109.66 25.19 20 22 25 3 356.67 3.61 21 22 26 4 200.69 14.79 22 22 69 47 112.95 26.50 23 22 70 48 112.77 26.41 24 22 71 49 112.81 26.38 25 23 26 3 334.16 0.14 26 23 35 12 113.20 26.39 27 23 37 14 114.23 25.85 28 23 69 46 113.03 26.49 29 23 71 48 113.05 26.30 30 23 101 78 114.49 25.77 31 23 104 81 114.59 25.75 32 23 105 82 114.45 25.80 33 23 108 85 115.25 26.04 34 24 71 47 114.29 25.84 35 24 101 77 114.49 25.78 36 24 104 80 114.54 25.77 37 24 108 84 115.53 26.09 38 26 69 43 116.16 26.32 39 26 108 82 152.91 8.65 40 27 30 3 356.44 5.66 41 27 31 4 321.55 2.48 42 27 69 42 531.44 2.44 43 28 31 3 334.59 0.64 44 28 108 80 177.40 3.58 45 32 112 80 453.75 1.33 46 33 112 79 453.75 1.34 47 33 113 80 453.75 1.34 48 33 211 178 33.13 0.29 49 34 113 79 453.75 1.34 50 34 115 81 453.75 1.34 51 34 207 173 60.79 8.39 52 35 112 77 524.70 4.08 53 35 113 78 458.86 0.67 54 35 114 79 453.76 1.34 55 35 115 80 453.75 1.34 56 36 115 79 453.75 1.34 57 36 116 80 453.75 1.34 58 36 117 81 453.75 1.34 59 36 203 167 81.25 8.68 60 37 115 78 455.42 0.93 61 37 116 79 453.76 1.34 62 37 117 80 453.76 1.34 63 38 117 79 453.76 1.34 64 38 118 80 453.75 1.34 65 38 119 81 453.76 1.34 66 39 117 78 455.12 0.86 67 39 118 79 453.75 1.34 68 39 119 80 453.75 1.34 69 39 122 83 361.06 0.27 70 39 125 86 359.41 0.26 71 40 119 79 453.76 1.34 72 40 122 82 361.19 0.23 73 41 119 78 453.84 1.36 74 41 120 79 453.76 1.34 75 41 122 81 390.87 1.54 76 42 121 79 453.75 1.34 77 44 119 75 455.38 0.95 78 51 119 68 453.72 1.35 79 51 147 96 307.87 1.24 80 51 191 140 90.95 9.04 81 51 192 141 90.67 9.04 82 51 195 144 89.72 8.96 83 54 195 141 89.95 8.85 84 54 196 142 89.74 8.96 85 55 145 90 308.25 1.22 86 55 147 92 307.88 1.23 87 55 195 140 89.73 8.96 88 55 200 145 86.40 10.51 89 55 203 148 83.88 9.81 90 58 196 138 89.74 8.96 91 58 200 142 87.48 9.94 92 59 115 56 453.94 1.42 93 59 200 141 86.38 10.48 94 59 203 144 81.23 8.68 95 59 204 145 81.17 8.68 96 62 204 142 81.17 8.66 97 63 204 141 81.17 8.66 98 63 207 144 61.37 8.60 99 73 125 52 359.39 0.26 100 77 121 44 453.72 1.34 101 77 122 45 444.97 2.53 102 77 125 48 359.85 0.18 103 79 121 42 453.72 1.36 104 80 121 41 453.83 1.36 105 83 121 38 455.17 0.70 106 84 121 37 454.50 1.03 107 84 182 98 130.59 25.02 108 85 182 97 131.25 25.26 109 88 124 36 425.76 1.18 110 88 128 40 359.53 0.18 111 88 131 43 359.29 0.21 112 88 132 44 359.09 0.29 113 88 151 63 284.06 1.35 114 89 121 32 453.75 1.31 115 89 124 35 384.50 0.30 116 89 151 62 284.06 1.35 117 90 121 31 453.72 1.31 118 90 125 35 361.04 0.24 119 94 125 31 359.40 0.26 120 95 125 30 359.39 0.26 121 95 128 33 353.12 0.46 122 95 129 34 337.02 2.83 123 95 132 37 315.26 0.24 124 98 116 18 460.20 1.75 125 98 125 27 359.38 0.26 126 98 126 28 359.12 0.29 127 98 129 31 323.53 3.91 128 99 129 30 323.52 3.92 129 99 132 33 314.41 0.34 130 99 133 34 311.49 0.99 131 102 114 12 517.80 3.47 132 102 116 14 453.78 1.33 133 102 129 27 323.53 3.91 134 102 130 28 323.49 3.91 135 102 133 31 309.43 1.05 136 102 137 35 309.29 1.02 137 102 141 39 309.05 1.06 138 103 137 34 309.21 1.01 139 105 114 9 479.89 8.10 140 106 137 31 309.17 0.99 141 106 140 34 309.04 1.05 142 109 112 3 453.75 1.33 143 110 140 30 309.03 1.06 144 111 211 100 38.24 2.19 145 112 211 99 33.15 0.30 146 113 140 27 309.03 1.05 147 113 142 29 308.75 1.10 148 113 207 94 60.79 8.39 149 113 210 97 38.26 2.19 150 113 211 98 33.13 0.29 151 114 137 23 309.28 1.02 152 114 140 26 309.04 1.05 153 114 141 27 308.99 1.06 154 114 142 28 308.99 1.06 155 115 141 26 309.03 1.06 156 115 142 27 309.00 1.06 157 115 143 28 308.64 1.19 158 115 203 88 81.25 8.68 159 115 207 92 61.38 8.69 160 116 130 14 315.07 0.28 161 116 141 25 309.08 1.07 162 116 143 27 309.00 1.07 163 116 144 28 308.11 1.15 164 116 145 29 308.09 1.14 165 116 203 87 82.25 8.99 166 117 144 27 308.82 1.15 167 117 145 28 308.13 1.16 168 118 122 4 361.30 0.18 169 118 123 5 360.94 0.29 170 118 145 27 308.67 1.23 171 118 146 28 308.28 1.36 172 118 147 29 307.94 1.21 173 119 122 3 361.39 0.15 174 119 123 4 361.32 0.18 175 119 147 28 307.88 1.24 176 119 188 69 92.67 8.97 177 119 189 70 92.46 9.02 178 119 191 72 91.28 9.19 179 120 123 3 363.55 1.14 180 120 124 4 363.49 1.17 181 120 147 27 308.57 1.27 182 120 148 28 307.86 1.23 183 120 150 30 292.40 1.43 184 120 188 68 92.54 9.04 185 121 124 3 363.49 1.17 186 121 125 4 361.67 0.28 187 121 150 29 289.46 1.28 188 122 125 3 369.07 3.98 189 122 126 4 361.60 0.32 190 123 126 3 363.42 1.15 191 123 127 4 361.68 0.28 192 123 146 23 308.57 1.27 193 123 147 24 308.56 1.27 194 123 149 26 289.45 1.28 195 124 127 3 360.94 0.50 196 124 128 4 360.88 0.47 197 124 149 25 298.76 0.92 198 124 150 26 284.06 1.35 199 124 151 27 282.70 1.77 200 125 128 3 371.00 4.54 201 125 129 4 355.91 2.93 202 126 129 3 372.70 3.69 203 126 130 4 372.69 3.69 204 126 146 20 308.62 1.24 205 127 130 3 372.70 3.69 206 127 131 4 351.75 6.79 207 127 149 22 299.06 0.77 208 127 159 32 218.66 0.52 209 127 160 33 218.66 0.52 210 128 131 3 362.68 1.32 211 128 132 4 352.32 6.50 212 129 132 3 358.30 3.81 213 129 133 4 338.85 0.35 214 130 133 3 343.62 2.73 215 130 138 8 309.33 1.03 216 130 141 11 309.35 1.03 217 130 144 14 309.04 1.07 218 130 159 29 218.66 0.52 219 130 162 32 218.14 0.67 220 131 138 7 309.67 1.11 221 131 160 29 218.47 0.60 222 131 161 30 218.25 0.71 223 133 137 4 334.99 2.20 224 133 138 5 329.58 4.90 225 133 141 8 315.63 2.08 226 134 137 3 364.57 0.86 227 134 138 4 364.62 0.88 228 135 138 3 364.62 0.88 229 135 139 4 349.00 8.69 230 136 139 3 365.36 0.52 231 136 140 4 365.36 0.52 232 137 140 3 370.64 2.13 233 137 141 4 354.49 5.95 234 138 141 3 370.25 2.33 235 138 161 23 218.38 0.57 236 138 162 24 218.03 0.68 237 139 166 27 216.18 0.15 238 141 144 3 420.25 2.31 239 141 162 21 218.12 0.63 240 141 166 25 216.16 0.15 241 142 162 20 218.38 0.56 242 142 166 24 216.16 0.15 243 142 206 64 65.64 6.57 244 142 207 65 61.38 8.69 245 142 210 68 38.65 1.98 246 143 162 19 218.38 0.55 247 143 166 23 216.15 0.15 248 143 202 59 87.53 9.90 249 143 203 60 85.14 10.44 250 143 206 63 65.88 10.84 251 144 159 15 218.67 0.51 252 144 162 18 218.47 0.49 253 144 166 22 216.19 0.14 254 144 167 23 216.13 0.14 255 144 168 24 216.09 0.14 256 144 202 58 87.59 9.93 257 144 203 59 85.16 10.44 258 145 168 23 216.09 0.15 259 145 170 25 215.97 0.10 260 145 199 54 88.56 9.53 261 145 202 57 87.62 9.94 262 145 203 58 86.23 10.55 263 146 149 3 367.49 0.76 264 146 159 13 218.70 0.49 265 146 168 22 216.13 0.14 266 146 169 23 216.05 0.14 267 146 170 24 215.84 0.19 268 147 170 23 215.69 0.12 269 147 191 44 91.66 9.00 270 147 194 47 90.87 8.98 271 147 195 48 90.81 9.04 272 147 199 52 90.67 9.04 273 148 170 22 216.03 0.13 274 148 171 23 215.72 0.12 275 148 175 27 215.59 0.18 276 148 177 29 215.62 0.14 277 148 178 30 215.35 0.21 278 148 188 40 92.72 8.95 279 148 191 43 91.77 8.96 280 149 152 3 347.11 7.46 281 149 155 6 322.46 2.29 282 149 158 9 219.36 0.67 283 149 159 10 218.94 0.47 284 149 169 20 216.13 0.14 285 149 171 22 216.03 0.14 286 149 177 28 215.58 0.18 287 149 178 29 215.01 0.07 288 150 154 4 379.46 0.08 289 150 177 27 215.49 0.14 290 150 182 32 130.66 24.99 291 151 154 3 348.17 5.95 292 151 155 4 331.25 0.43 293 152 155 3 371.60 1.76 294 152 156 4 326.98 0.04 295 152 157 5 219.90 0.65 296 152 169 17 216.40 0.12 297 152 171 19 216.09 0.15 298 152 178 26 215.25 0.06 299 153 156 3 331.25 0.43 300 153 178 25 215.91 0.11 301 153 179 26 215.16 0.07 302 153 180 27 215.11 0.09 303 154 180 26 211.28 1.82 304 155 158 3 354.00 7.06 305 155 160 5 219.53 0.66 306 157 169 12 216.37 0.11 307 158 162 4 348.44 9.06 308 158 163 5 270.94 23.29 309 158 164 6 219.31 0.68 310 159 162 3 363.18 1.70 311 159 167 8 217.07 0.45 312 162 166 4 345.89 6.94 313 162 167 5 338.75 10.52 314 163 166 3 369.85 1.20 315 163 167 4 345.00 7.38 316 164 167 3 365.18 1.13 317 165 202 37 88.89 9.37 318 165 206 41 84.97 10.35 319 166 202 36 88.47 9.52 320 166 210 44 61.33 8.72 321 167 202 35 88.52 9.54 322 168 202 34 88.44 9.59 323 170 191 21 92.12 8.82 324 170 194 24 91.03 8.98 325 170 198 28 91.02 8.98 326 170 199 29 90.83 8.98 327 171 191 20 92.89 8.95 328 172 187 15 98.95 10.63 329 172 190 18 98.45 10.90 330 172 191 19 94.90 9.49 331 172 194 22 92.55 8.88 332 173 187 14 99.54 10.85 333 174 185 11 105.97 12.97 334 174 187 13 99.54 10.85 335 175 187 12 99.15 10.67 336 175 188 13 99.15 10.67 337 175 191 16 99.14 10.67 338 176 181 5 450.56 5.75 339 176 183 7 328.79 2.21 340 177 181 4 405.26 1.11 341 177 182 5 351.19 7.57 342 177 183 6 328.79 2.21 343 177 188 11 99.12 10.66 344 184 188 4 344.55 2.50 345 184 189 5 346.05 8.90 346 185 188 3 371.31 0.21 347 186 189 3 371.31 0.20 348 186 190 4 370.88 0.01 349 187 190 3 371.30 0.21 350 187 191 4 376.53 2.45 351 188 191 3 407.45 3.00 352 190 193 3 423.59 0.94 353 191 194 3 369.28 0.76 354 191 195 4 352.78 7.49 355 192 195 3 374.35 1.01 356 192 196 4 354.39 6.68 357 193 196 3 371.55 0.39 358 193 197 4 350.20 8.77 359 193 198 5 347.63 10.05 360 194 197 3 367.81 0.04 361 194 198 4 347.62 10.05 362 194 199 5 345.84 10.93 363 194 200 6 345.85 10.93 364 195 199 4 346.28 10.72 365 195 200 5 346.28 10.72 366 196 200 4 353.37 7.17 367 197 200 3 377.02 2.44 368 197 201 4 336.58 2.19 369 198 201 3 350.50 7.67 370 198 202 4 338.06 1.45 371 199 202 3 373.31 3.73 372 199 203 4 338.06 1.45 373 200 203 3 339.25 0.83 374 200 204 4 335.47 1.81 375 201 204 3 371.47 0.33 376 201 205 4 334.52 2.29 377 202 205 3 345.06 2.98 378 202 206 4 338.32 0.40 379 203 206 3 340.69 1.53 380 203 207 4 339.13 0.79 381 204 207 3 355.25 7.27 382 204 208 4 339.14 0.79 383 205 208 3 350.93 4.91 384 205 209 4 334.65 3.05 385 206 209 3 369.31 1.51 386 206 210 4 333.24 3.75 387 207 210 3 368.69 0.17 388 207 211 4 332.33 3.50 389 208 211 3 332.30 3.49 390 208 212 4 321.98 1.18 391 208 213 5 188.44 16.37