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 61.43 0.93 2 18 46 28 61.45 0.92 3 18 47 29 61.45 0.92 4 18 48 30 50.80 2.60 5 18 49 31 56.05 0.24 6 18 53 35 43.43 1.09 7 19 46 27 62.11 0.96 8 19 47 28 61.55 0.86 9 20 47 27 63.02 0.57 10 20 48 28 62.40 0.82 11 20 60 40 61.41 0.74 12 20 70 50 61.40 0.74 13 20 71 51 62.45 0.85 14 20 72 52 63.01 0.57 15 21 24 3 364.80 1.45 16 21 25 4 333.99 2.42 17 21 47 26 64.05 0.17 18 21 71 50 63.44 0.36 19 22 25 3 354.95 6.38 20 22 26 4 333.87 2.35 21 22 69 47 63.94 0.11 22 22 70 48 63.61 0.38 23 22 71 49 64.08 0.16 24 23 26 3 354.80 7.71 25 23 35 12 64.10 0.15 26 23 69 46 64.10 0.14 27 23 71 48 64.11 0.15 28 23 101 78 68.38 1.02 29 23 104 81 68.50 1.05 30 23 105 82 67.64 0.82 31 23 108 85 68.54 1.10 32 24 71 47 68.03 1.17 33 24 101 77 68.55 1.04 34 24 104 80 68.67 1.01 35 24 108 84 97.08 15.20 36 26 69 43 96.33 14.86 37 26 108 82 182.12 23.62 38 27 30 3 353.91 3.64 39 27 31 4 345.60 7.79 40 27 69 42 533.76 3.98 41 28 31 3 379.69 0.82 42 28 108 80 189.25 19.88 43 32 112 80 454.81 1.44 44 33 112 79 454.82 1.44 45 33 113 80 454.81 1.44 46 33 211 178 35.60 0.53 47 34 113 79 454.83 1.44 48 34 115 81 454.81 1.44 49 34 207 173 80.28 0.56 50 34 211 177 35.55 0.52 51 35 112 77 523.53 0.60 52 35 113 78 460.99 0.28 53 35 114 79 454.84 1.45 54 35 115 80 454.82 1.44 55 36 115 79 454.84 1.45 56 36 116 80 454.82 1.44 57 36 117 81 454.82 1.45 58 36 203 167 103.75 0.06 59 37 115 78 455.62 1.53 60 37 116 79 454.85 1.45 61 37 117 80 454.85 1.45 62 38 117 79 454.85 1.45 63 38 118 80 454.84 1.45 64 38 119 81 454.84 1.45 65 39 117 78 455.17 1.40 66 39 118 79 454.84 1.45 67 39 119 80 454.85 1.45 68 39 122 83 364.61 0.07 69 39 125 86 362.75 0.94 70 40 119 79 454.86 1.45 71 40 122 82 364.69 0.04 72 41 119 78 455.01 1.41 73 41 120 79 454.86 1.45 74 42 121 79 454.85 1.44 75 44 119 75 455.20 1.36 76 51 119 68 454.83 1.46 77 51 147 96 308.08 0.03 78 51 191 140 115.69 2.25 79 51 192 141 115.11 2.33 80 51 195 144 108.77 1.01 81 54 195 141 108.75 1.01 82 54 196 142 108.75 1.01 83 55 147 92 308.11 0.01 84 55 195 140 108.72 0.99 85 55 200 145 108.23 0.86 86 55 203 148 107.23 0.96 87 58 196 138 108.72 1.01 88 58 200 142 108.21 0.85 89 59 115 56 455.01 1.41 90 59 203 144 102.75 0.56 91 59 204 145 101.75 0.39 92 62 204 142 101.77 0.39 93 62 208 146 84.45 1.50 94 63 204 141 101.77 0.39 95 63 207 144 84.46 1.49 96 73 125 52 362.77 0.93 97 77 121 44 454.83 1.45 98 77 122 45 451.07 1.35 99 77 125 48 364.19 0.22 100 79 121 42 454.85 1.44 101 80 121 41 455.07 1.43 102 83 121 38 455.07 1.47 103 84 121 37 455.06 1.46 104 84 182 98 146.72 2.65 105 85 182 97 154.04 0.94 106 87 151 64 304.36 1.55 107 88 124 36 432.24 7.43 108 88 128 40 363.78 0.47 109 88 131 43 363.18 0.70 110 88 132 44 362.92 0.71 111 88 151 63 293.13 1.07 112 89 121 32 454.92 1.47 113 89 124 35 379.85 1.77 114 89 151 62 293.12 1.08 115 90 121 31 454.83 1.44 116 90 125 35 364.88 0.07 117 94 125 31 362.78 0.93 118 95 125 30 362.77 0.92 119 95 128 33 358.70 0.29 120 95 129 34 337.09 0.40 121 95 132 37 323.51 1.19 122 98 125 27 362.65 0.98 123 98 126 28 362.32 1.00 124 98 129 31 328.21 0.79 125 99 129 30 328.20 0.80 126 99 132 33 322.31 1.56 127 99 133 34 311.31 0.21 128 102 114 12 533.74 0.29 129 102 116 14 455.11 1.39 130 102 129 27 323.87 1.33 131 102 130 28 323.54 1.18 132 102 133 31 311.31 0.21 133 102 137 35 311.11 0.26 134 102 141 39 310.83 0.27 135 103 137 34 311.11 0.26 136 105 114 9 456.34 1.30 137 106 137 31 311.06 0.25 138 106 140 34 310.85 0.26 139 109 112 3 454.84 1.45 140 110 140 30 310.82 0.26 141 111 211 100 39.62 0.32 142 113 140 27 310.83 0.27 143 113 142 29 310.49 0.21 144 113 207 94 80.31 0.55 145 113 210 97 41.28 0.51 146 113 211 98 36.73 1.10 147 114 137 23 311.10 0.26 148 114 140 26 310.83 0.27 149 114 141 27 310.74 0.27 150 114 142 28 310.54 0.18 151 115 141 26 310.81 0.27 152 115 142 27 310.74 0.27 153 115 143 28 310.26 0.18 154 115 203 88 104.64 0.40 155 115 207 92 81.60 0.10 156 116 130 14 323.52 1.19 157 116 141 25 310.83 0.27 158 116 143 27 310.53 0.21 159 116 144 28 310.05 0.21 160 116 145 29 309.57 0.01 161 116 203 87 105.42 0.72 162 117 144 27 310.38 0.23 163 117 145 28 310.07 0.24 164 118 122 4 364.63 0.07 165 118 123 5 364.50 0.12 166 118 145 27 310.39 0.23 167 118 146 28 310.03 0.21 168 118 147 29 308.12 0.04 169 119 122 3 367.88 0.99 170 119 123 4 364.72 0.06 171 119 147 28 308.12 0.03 172 119 188 69 117.50 2.58 173 119 189 70 117.48 2.58 174 119 191 72 115.73 2.27 175 120 123 3 370.47 0.26 176 120 124 4 367.49 1.19 177 120 147 27 310.23 0.27 178 120 148 28 308.13 0.03 179 120 150 30 302.76 2.44 180 120 188 68 117.53 2.56 181 121 124 3 367.52 1.21 182 121 125 4 365.12 0.02 183 121 150 29 294.38 1.70 184 122 125 3 370.39 1.56 185 122 126 4 365.12 0.04 186 123 126 3 370.69 2.75 187 123 127 4 365.14 0.03 188 123 146 23 310.32 0.23 189 123 147 24 310.21 0.28 190 123 149 26 294.47 1.66 191 124 127 3 370.81 2.69 192 124 128 4 364.58 0.26 193 124 149 25 298.22 0.21 194 124 150 26 293.13 1.07 195 124 151 27 293.03 1.09 196 125 128 3 365.50 0.02 197 125 129 4 365.31 0.11 198 126 129 3 372.95 2.79 199 126 130 4 365.31 0.11 200 126 146 20 310.36 0.25 201 127 130 3 372.65 2.63 202 127 131 4 364.17 0.46 203 127 149 22 298.90 0.56 204 127 159 32 224.29 1.00 205 128 131 3 367.13 0.87 206 128 132 4 364.15 0.46 207 129 132 3 365.20 1.00 208 129 133 4 364.07 0.48 209 130 133 3 364.49 0.28 210 130 138 8 311.11 0.26 211 130 141 11 311.07 0.28 212 130 144 14 310.81 0.28 213 130 159 29 224.29 1.00 214 130 162 32 223.50 1.02 215 131 138 7 311.50 0.24 216 131 160 29 224.28 0.99 217 131 161 30 224.27 0.98 218 133 137 4 348.76 8.05 219 133 138 5 317.66 3.01 220 133 141 8 311.57 0.24 221 134 137 3 381.97 0.03 222 134 138 4 333.68 1.78 223 135 138 3 369.38 1.22 224 135 139 4 333.68 1.78 225 136 140 4 366.17 0.38 226 137 140 3 377.85 2.32 227 137 141 4 368.08 1.33 228 138 141 3 380.69 3.74 229 138 161 23 223.58 1.02 230 138 162 24 223.44 1.01 231 139 166 27 221.97 1.50 232 141 162 21 223.46 1.01 233 141 166 25 221.82 1.45 234 142 162 20 223.54 1.01 235 142 166 24 221.75 1.43 236 142 206 64 83.90 0.24 237 142 207 65 81.95 0.15 238 142 210 68 79.08 0.86 239 143 162 19 223.58 1.02 240 143 166 23 221.77 1.46 241 143 202 59 108.23 0.86 242 143 203 60 106.27 0.58 243 143 206 63 86.09 1.33 244 144 159 15 224.28 0.99 245 144 162 18 223.46 1.00 246 144 166 22 221.86 1.46 247 144 167 23 221.66 1.46 248 144 168 24 221.66 1.46 249 144 202 58 108.56 1.01 250 144 203 59 107.73 1.05 251 145 168 23 221.65 1.46 252 145 170 25 221.56 1.49 253 145 199 54 108.72 0.99 254 145 202 57 108.59 0.99 255 145 203 58 108.53 1.02 256 146 149 3 372.54 0.86 257 146 159 13 224.30 0.99 258 146 167 21 221.84 1.47 259 146 168 22 221.70 1.47 260 146 169 23 221.63 1.47 261 146 170 24 221.56 1.49 262 147 170 23 221.32 1.44 263 147 191 44 115.72 2.27 264 147 194 47 115.13 2.32 265 147 195 48 115.40 2.19 266 147 199 52 115.09 2.33 267 148 170 22 221.65 1.46 268 148 171 23 221.36 1.43 269 148 175 27 221.27 1.47 270 148 177 29 221.19 1.50 271 148 178 30 220.79 1.39 272 148 188 40 117.48 2.58 273 148 191 43 115.88 2.21 274 149 152 3 368.79 0.02 275 149 155 6 317.69 0.73 276 149 158 9 224.56 1.07 277 149 159 10 224.56 1.07 278 149 169 20 221.70 1.47 279 149 171 22 221.47 1.48 280 149 177 28 221.27 1.45 281 149 178 29 220.56 1.33 282 150 154 4 382.62 2.52 283 150 177 27 220.90 1.38 284 151 154 3 372.15 1.02 285 151 155 4 332.01 3.50 286 152 155 3 369.44 0.34 287 152 156 4 332.02 0.48 288 152 157 5 226.37 1.46 289 152 169 17 222.00 1.48 290 152 171 19 221.74 1.45 291 152 178 26 220.65 1.35 292 153 156 3 341.13 1.06 293 153 178 25 221.44 1.36 294 153 179 26 220.58 1.33 295 153 180 27 220.05 1.08 296 154 180 26 220.04 1.09 297 155 158 3 367.74 1.24 298 155 160 5 227.29 1.82 299 157 169 12 222.02 1.48 300 158 162 4 371.00 1.22 301 158 163 5 248.19 3.17 302 158 164 6 223.97 0.74 303 159 162 3 371.05 1.24 304 159 167 8 222.07 1.48 305 162 166 4 370.65 1.63 306 162 167 5 325.02 4.20 307 163 166 3 377.12 1.61 308 163 167 4 346.95 10.22 309 164 167 3 358.51 4.44 310 165 202 37 108.73 0.95 311 165 206 41 106.53 0.49 312 166 202 36 108.70 0.96 313 167 202 35 108.73 0.96 314 168 202 34 108.73 0.96 315 170 191 21 115.74 2.27 316 170 194 24 115.14 2.31 317 170 198 28 115.31 2.42 318 170 199 29 115.12 2.33 319 171 191 20 117.33 2.42 320 172 187 15 119.39 1.82 321 172 190 18 118.97 1.85 322 172 191 19 118.91 1.82 323 173 187 14 127.20 1.79 324 174 185 11 146.73 2.71 325 174 187 13 130.72 0.91 326 175 187 12 121.68 0.97 327 175 188 13 121.67 0.97 328 175 191 16 121.67 0.97 329 176 181 5 438.75 8.30 330 176 183 7 355.16 13.28 331 176 185 9 146.60 2.65 332 177 181 4 406.56 2.41 333 177 182 5 378.60 1.55 334 177 183 6 363.25 9.22 335 177 188 11 120.06 2.04 336 184 188 4 346.89 1.68 337 184 189 5 350.12 0.07 338 185 188 3 383.60 0.94 339 186 189 3 387.25 0.89 340 186 190 4 387.26 0.89 341 187 190 3 387.26 0.89 342 187 191 4 388.55 0.24 343 188 191 3 419.70 0.68 344 190 193 3 445.34 5.75 345 191 194 3 380.39 0.55 346 191 195 4 369.19 1.20 347 192 195 3 378.94 4.58 348 192 196 4 369.19 1.20 349 193 196 3 369.93 0.84 350 193 197 4 352.60 9.50 351 193 198 5 331.05 0.99 352 194 197 3 380.93 3.58 353 194 198 4 331.00 1.01 354 194 199 5 330.95 0.99 355 194 200 6 330.96 0.99 356 195 199 4 327.00 2.34 357 195 200 5 327.80 2.74 358 196 200 4 351.57 8.25 359 197 200 3 376.50 1.35 360 197 201 4 334.64 1.19 361 198 201 3 365.25 1.40 362 198 202 4 334.64 1.20 363 199 202 3 369.48 0.97 364 199 203 4 349.10 2.03 365 200 203 3 363.12 5.00 366 200 204 4 335.56 0.46 367 201 204 3 370.81 2.08 368 201 205 4 336.50 0.05 369 202 205 3 355.01 8.30 370 202 206 4 336.74 0.17 371 203 206 3 369.88 0.87 372 203 207 4 336.80 0.80 373 204 207 3 367.60 0.42 374 204 208 4 367.59 0.42 375 205 208 3 367.62 0.42 376 205 209 4 367.61 0.41 377 206 209 3 372.81 2.19 378 206 210 4 372.81 2.19 379 207 210 3 380.35 2.50 380 207 211 4 335.26 1.54 381 208 211 3 372.23 2.12 382 208 212 4 191.16 22.61 383 208 213 5 187.49 24.44