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 64.94 0.30 2 18 46 28 64.86 0.35 3 18 47 29 64.85 0.35 4 18 48 30 54.98 0.68 5 18 49 31 59.43 0.50 6 18 53 35 46.38 0.85 7 19 46 27 65.08 0.24 8 19 47 28 64.86 0.35 9 20 47 27 66.92 0.70 10 20 48 28 66.11 0.41 11 20 60 40 64.83 0.33 12 20 65 45 66.34 0.55 13 20 70 50 64.81 0.33 14 20 71 51 65.89 0.29 15 20 72 52 66.79 0.74 16 21 24 3 379.19 0.70 17 21 25 4 316.47 30.66 18 21 47 26 67.47 0.67 19 21 71 50 67.11 0.75 20 22 25 3 359.39 9.21 21 22 26 4 228.94 0.53 22 22 69 47 67.17 0.78 23 22 70 48 67.38 0.68 24 22 71 49 67.48 0.65 25 23 26 3 359.07 9.37 26 23 35 12 67.73 0.74 27 23 37 14 68.14 0.59 28 23 69 46 67.72 0.76 29 23 71 48 67.78 0.72 30 23 101 78 70.36 0.14 31 23 104 81 70.46 0.12 32 23 105 82 69.67 0.36 33 23 108 85 71.33 0.31 34 24 71 47 68.96 0.21 35 24 101 77 70.39 0.14 36 24 108 84 72.12 0.01 37 26 69 43 71.00 0.23 38 26 108 82 188.34 21.39 39 27 30 3 347.55 2.30 40 27 31 4 340.46 0.35 41 27 69 42 538.23 0.98 42 28 31 3 362.16 9.61 43 28 108 80 190.33 20.41 44 32 112 80 461.00 1.47 45 33 112 79 461.00 1.47 46 33 113 80 461.00 1.47 47 33 212 179 21.71 0.07 48 33 213 180 21.36 0.09 49 34 113 79 461.00 1.48 50 34 115 81 460.99 1.48 51 34 207 173 80.92 0.24 52 34 212 178 21.89 0.16 53 35 112 77 539.56 0.48 54 35 113 78 463.07 1.22 55 35 114 79 461.01 1.48 56 35 115 80 461.00 1.48 57 36 115 79 461.01 1.48 58 36 116 80 461.00 1.48 59 36 117 81 461.00 1.48 60 36 203 167 105.11 0.42 61 37 115 78 461.84 1.52 62 37 116 79 461.01 1.48 63 37 117 80 461.01 1.48 64 38 117 79 461.01 1.48 65 38 118 80 461.00 1.48 66 38 119 81 461.01 1.48 67 38 147 109 313.67 0.23 68 39 117 78 461.16 1.47 69 39 118 79 461.01 1.48 70 39 119 80 461.01 1.48 71 39 122 83 369.26 0.66 72 39 125 86 368.54 0.41 73 40 119 79 461.02 1.48 74 40 122 82 369.39 0.63 75 41 119 78 461.07 1.48 76 41 120 79 461.01 1.48 77 42 121 79 461.00 1.46 78 44 119 75 461.32 1.50 79 51 119 68 460.90 1.52 80 51 147 96 313.27 0.25 81 51 191 140 112.85 0.42 82 51 192 141 112.75 0.44 83 51 195 144 109.06 1.15 84 54 195 141 110.09 0.63 85 54 196 142 109.06 1.14 86 55 147 92 313.29 0.25 87 55 195 140 109.06 1.13 88 55 200 145 108.42 0.96 89 55 203 148 107.64 0.76 90 58 196 138 109.27 1.02 91 58 200 142 108.48 0.98 92 58 204 146 105.03 0.38 93 59 115 56 461.05 1.48 94 59 203 144 105.11 0.42 95 59 204 145 104.61 0.29 96 62 204 142 104.62 0.29 97 62 208 146 85.92 0.97 98 63 204 141 104.64 0.29 99 63 207 144 85.15 0.69 100 73 125 52 368.54 0.41 101 77 121 44 460.93 1.47 102 77 122 45 457.17 2.29 103 77 125 48 369.44 0.23 104 79 121 42 461.01 1.46 105 80 121 41 461.12 1.50 106 83 121 38 461.14 1.51 107 84 121 37 461.13 1.51 108 84 182 98 173.12 7.11 109 85 182 97 173.83 6.77 110 87 151 64 311.05 0.56 111 88 124 36 453.89 2.44 112 88 128 40 368.63 0.42 113 88 131 43 368.52 0.42 114 88 132 44 368.25 0.29 115 88 151 63 299.25 0.66 116 89 121 32 461.09 1.49 117 89 124 35 425.19 16.80 118 89 151 62 300.24 0.17 119 90 121 31 460.93 1.45 120 90 125 35 369.82 0.39 121 94 125 31 368.59 0.43 122 95 125 30 368.59 0.43 123 95 128 33 363.53 0.74 124 95 129 34 334.99 1.45 125 95 132 37 328.67 1.25 126 98 125 27 368.51 0.40 127 98 126 28 368.30 0.39 128 98 129 31 331.78 0.15 129 99 129 30 331.76 0.15 130 99 132 33 327.94 1.12 131 99 133 34 317.75 1.29 132 102 114 12 535.73 0.71 133 102 116 14 461.08 1.49 134 102 129 27 328.91 1.28 135 102 130 28 328.89 1.28 136 102 133 31 314.74 0.21 137 102 137 35 314.58 0.18 138 102 141 39 314.30 0.28 139 103 137 34 314.57 0.18 140 105 114 9 488.86 12.38 141 106 137 31 314.55 0.18 142 106 140 34 314.29 0.27 143 109 112 3 460.99 1.47 144 110 140 30 314.28 0.28 145 111 212 101 27.80 0.23 146 111 213 102 22.04 0.22 147 112 213 101 22.01 0.24 148 113 142 29 313.90 0.21 149 113 207 94 81.31 0.42 150 113 210 97 44.61 1.85 151 113 212 99 23.06 0.48 152 114 137 23 314.60 0.20 153 114 140 26 314.29 0.28 154 114 141 27 314.10 0.27 155 114 142 28 314.10 0.27 156 115 141 26 314.26 0.27 157 115 142 27 314.12 0.26 158 115 143 28 313.94 0.28 159 115 203 88 105.20 0.46 160 115 207 92 84.98 0.79 161 116 130 14 328.66 1.40 162 116 141 25 314.33 0.27 163 116 143 27 314.18 0.27 164 116 144 28 313.66 0.23 165 116 145 29 313.66 0.23 166 116 203 87 106.13 0.37 167 117 144 27 314.06 0.24 168 117 145 28 313.67 0.23 169 118 122 4 369.81 0.56 170 118 123 5 368.91 0.52 171 118 145 27 314.01 0.22 172 118 146 28 313.63 0.21 173 118 147 29 313.29 0.25 174 119 122 3 375.20 2.14 175 119 123 4 369.79 0.56 176 119 147 28 313.29 0.25 177 119 188 69 121.56 0.40 178 119 189 70 120.28 1.02 179 119 191 72 113.03 0.49 180 120 123 3 379.50 2.54 181 120 124 4 372.17 0.59 182 120 147 27 313.83 0.22 183 120 148 28 312.59 0.59 184 120 150 30 300.57 0.34 185 120 188 68 121.55 0.40 186 121 124 3 373.12 0.65 187 121 125 4 370.03 0.48 188 121 150 29 301.48 0.79 189 122 125 3 372.85 0.93 190 122 126 4 370.05 0.48 191 123 126 3 377.55 3.27 192 123 127 4 369.82 0.62 193 123 146 23 313.93 0.18 194 123 147 24 313.82 0.21 195 123 149 26 300.29 0.19 196 124 127 3 372.95 0.94 197 124 128 4 369.39 0.84 198 124 149 25 301.49 0.78 199 124 150 26 299.31 0.64 200 124 151 27 297.47 1.52 201 125 128 3 377.85 0.86 202 125 129 4 362.96 4.05 203 126 129 3 373.01 0.76 204 126 130 4 362.31 4.38 205 126 146 20 314.08 0.26 206 127 130 3 379.58 2.53 207 127 131 4 369.60 2.46 208 127 149 22 304.91 0.88 209 127 159 32 226.82 0.15 210 128 131 3 373.38 0.58 211 128 132 4 366.00 4.25 212 129 132 3 374.63 0.07 213 129 133 4 354.00 0.23 214 130 133 3 376.55 1.02 215 130 138 8 314.64 0.21 216 130 141 11 314.59 0.18 217 130 144 14 314.31 0.24 218 130 159 29 226.81 0.16 219 130 162 32 226.50 0.16 220 131 138 7 315.45 0.28 221 131 160 29 226.79 0.15 222 131 161 30 226.72 0.18 223 133 137 4 359.43 5.70 224 133 138 5 320.00 1.84 225 133 141 8 315.55 0.30 226 134 137 3 377.74 2.15 227 134 138 4 360.61 6.29 228 135 138 3 377.61 2.21 229 135 139 4 329.76 3.04 230 136 140 4 360.18 6.52 231 137 140 3 379.93 1.29 232 137 141 4 377.86 2.33 233 138 141 3 380.88 0.82 234 138 161 23 226.63 0.21 235 138 162 24 226.41 0.19 236 139 166 27 225.81 0.01 237 141 144 3 412.61 1.39 238 141 162 21 226.44 0.18 239 141 166 25 225.74 0.04 240 142 166 24 225.71 0.04 241 142 206 64 86.78 1.33 242 142 207 65 85.33 0.62 243 142 210 68 80.58 0.27 244 143 162 19 226.55 0.18 245 143 166 23 225.71 0.04 246 143 202 59 108.50 0.98 247 143 203 60 106.62 0.46 248 143 206 63 90.38 0.47 249 144 159 15 226.82 0.16 250 144 162 18 226.55 0.18 251 144 166 22 225.83 0.03 252 144 167 23 225.69 0.04 253 144 168 24 225.65 0.02 254 144 202 58 108.56 1.01 255 144 203 59 108.08 0.79 256 145 168 23 225.63 0.01 257 145 170 25 225.48 0.01 258 145 199 54 108.84 0.97 259 145 202 57 108.76 0.96 260 145 203 58 108.54 1.02 261 146 149 3 378.34 2.04 262 146 159 13 226.82 0.15 263 146 167 21 225.81 0.04 264 146 168 22 225.74 0.03 265 146 169 23 225.62 0.02 266 146 170 24 225.48 0.01 267 147 170 23 225.37 0.07 268 147 191 44 113.03 0.49 269 147 194 47 112.60 0.35 270 147 195 48 112.58 0.35 271 147 199 52 112.27 0.21 272 148 170 22 225.66 0.02 273 148 171 23 225.47 0.01 274 148 175 27 225.37 0.07 275 148 177 29 225.24 0.02 276 148 178 30 224.24 0.04 277 148 188 40 121.49 0.43 278 148 191 43 116.71 0.73 279 149 152 3 370.66 0.68 280 149 155 6 351.28 9.42 281 149 158 9 227.08 0.24 282 149 169 20 225.74 0.02 283 149 171 22 225.50 0.03 284 149 177 28 225.28 0.04 285 149 178 29 223.79 0.07 286 150 154 4 385.56 1.04 287 150 177 27 224.63 0.29 288 150 182 32 172.08 6.58 289 151 154 3 372.08 0.03 290 151 155 4 351.29 9.43 291 152 155 3 381.92 2.87 292 152 156 4 351.26 9.41 293 152 157 5 227.81 0.48 294 152 169 17 226.04 0.04 295 152 171 19 225.77 0.02 296 152 178 26 224.43 0.24 297 153 156 3 358.12 6.11 298 153 178 25 225.47 0.04 299 153 179 26 223.80 0.07 300 153 180 27 221.41 0.55 301 154 180 26 221.05 1.22 302 155 158 3 373.25 1.46 303 155 160 5 227.70 0.42 304 157 169 12 226.09 0.07 305 158 162 4 358.53 5.13 306 158 163 5 248.16 3.20 307 158 164 6 227.85 0.33 308 159 162 3 370.80 0.99 309 159 167 8 227.43 0.14 310 162 166 4 357.39 12.81 311 162 167 5 289.07 14.52 312 163 166 3 376.42 0.47 313 163 167 4 347.72 10.60 314 164 167 3 345.61 9.27 315 165 202 37 108.87 0.96 316 165 206 41 106.45 0.54 317 166 202 36 108.78 0.96 318 167 202 35 108.83 0.96 319 168 202 34 108.83 0.96 320 170 191 21 117.30 0.46 321 170 194 24 112.54 0.33 322 170 198 28 112.49 0.32 323 170 199 29 112.44 0.29 324 171 191 20 121.31 0.49 325 172 187 15 127.83 1.11 326 172 190 18 121.83 0.36 327 172 191 19 121.49 0.42 328 173 187 14 131.43 0.19 329 174 185 11 153.41 0.52 330 174 187 13 131.50 0.15 331 175 187 12 131.14 0.34 332 175 188 13 131.12 0.34 333 175 191 16 131.13 0.34 334 176 181 5 445.50 13.10 335 176 183 7 336.85 1.72 336 176 185 9 153.52 0.50 337 177 181 4 402.94 3.13 338 177 182 5 365.67 9.53 339 177 183 6 328.73 1.39 340 177 188 11 131.10 0.33 341 184 188 4 342.53 1.78 342 184 189 5 342.51 1.79 343 185 188 3 383.00 3.02 344 186 189 3 383.00 3.02 345 187 190 3 386.87 1.08 346 187 191 4 386.87 1.08 347 188 191 3 412.73 2.81 348 190 193 3 428.94 1.19 349 191 194 3 384.02 3.52 350 191 195 4 336.72 0.17 351 192 195 3 379.27 4.42 352 192 196 4 357.78 8.95 353 193 196 3 368.16 9.97 354 193 197 4 356.02 9.83 355 193 198 5 333.60 1.88 356 194 197 3 381.92 3.10 357 194 198 4 333.58 1.88 358 194 199 5 333.62 1.90 359 194 200 6 333.62 1.90 360 195 199 4 333.62 1.90 361 195 200 5 333.62 1.90 362 196 200 4 342.76 3.80 363 197 200 3 388.75 0.43 364 197 201 4 357.39 11.10 365 198 201 3 357.42 11.09 366 198 202 4 357.47 11.06 367 199 202 3 362.52 8.54 368 199 203 4 358.05 10.78 369 200 203 3 362.52 8.54 370 200 204 4 358.06 10.78 371 201 204 3 377.44 1.08 372 201 205 4 355.03 8.30 373 202 205 3 359.30 6.17 374 202 206 4 355.03 8.30 375 203 206 3 363.71 3.97 376 203 207 4 337.49 0.46 377 204 207 3 370.62 2.22 378 204 208 4 337.41 0.42 379 205 208 3 356.58 4.80 380 205 209 4 336.82 0.71 381 206 209 3 349.79 5.11 382 206 210 4 342.66 2.16 383 207 210 3 378.91 0.87 384 207 211 4 325.97 2.27 385 207 212 5 247.99 6.72 386 208 211 3 304.70 21.63