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 16 139 137 37.62 0.21 2 16 140 138 37.59 0.20 3 16 142 140 38.79 0.40 4 16 143 141 45.41 0.82 5 16 144 142 47.07 1.01 6 16 156 154 44.03 0.89 7 16 157 155 44.12 0.99 8 16 158 156 45.30 0.90 9 16 189 191 45.94 1.23 10 16 190 192 37.59 0.20 11 16 194 196 37.59 0.20 12 17 143 140 47.35 1.06 13 17 144 141 47.35 1.06 14 17 145 142 48.16 1.06 15 17 146 143 50.23 0.96 16 17 187 188 47.49 1.08 17 17 188 189 47.28 1.10 18 17 189 190 46.69 1.16 19 17 191 192 46.72 1.17 20 17 220 220 47.09 1.19 21 17 221 221 47.34 1.03 22 18 156 152 54.60 0.70 23 18 188 188 47.43 1.07 24 19 157 152 49.56 1.76 25 19 158 153 47.34 1.06 26 19 188 187 49.65 1.75 27 20 156 150 77.98 1.70 28 20 157 151 57.34 1.14 29 21 144 137 83.56 0.03 30 21 152 145 87.86 1.77 31 21 154 147 87.87 1.77 32 21 155 148 83.56 0.03 33 21 156 149 82.50 0.01 34 22 26 4 297.88 0.97 35 22 27 5 296.53 0.29 36 22 139 131 83.56 0.03 37 22 154 146 93.98 0.12 38 22 155 147 86.67 1.34 39 22 156 148 83.73 0.12 40 22 157 149 83.54 0.03 41 23 26 3 313.81 1.45 42 23 27 4 297.88 0.97 43 23 71 56 205.77 0.42 44 23 154 145 94.54 0.28 45 24 27 3 296.54 0.29 46 24 28 4 295.52 0.15 47 24 30 6 290.60 1.06 48 24 69 53 203.56 1.49 49 24 70 54 205.81 0.43 50 24 71 55 205.81 0.43 51 24 117 107 203.08 1.16 52 24 155 145 95.36 0.68 53 25 28 3 296.50 0.27 54 25 116 105 205.70 0.45 55 25 117 106 205.31 0.48 56 27 30 3 302.62 2.79 57 27 137 124 144.03 0.68 58 27 139 126 137.77 2.45 59 27 155 142 181.19 1.02 60 27 157 144 137.80 2.46 61 28 116 102 206.35 0.36 62 28 117 103 206.34 0.36 63 28 118 104 205.92 0.39 64 28 119 105 205.83 0.43 65 29 45 20 258.84 0.63 66 29 46 21 239.06 2.25 67 29 119 104 205.93 0.39 68 29 120 105 205.83 0.43 69 29 121 106 205.81 0.43 70 29 198 187 177.60 0.21 71 29 200 189 187.66 0.12 72 29 207 196 189.05 0.48 73 30 40 14 289.12 1.25 74 30 43 17 263.41 0.29 75 30 44 18 262.99 0.43 76 30 68 46 263.05 0.42 77 30 139 123 188.00 0.13 78 30 140 124 189.06 0.56 79 30 141 125 189.99 0.24 80 30 155 139 189.94 0.23 81 30 198 186 178.85 0.24 82 31 43 16 263.48 0.29 83 31 44 17 263.33 0.27 84 31 45 18 262.99 0.43 85 31 52 25 262.91 0.45 86 31 66 43 263.13 0.43 87 31 67 44 263.09 0.41 88 31 68 45 263.05 0.42 89 32 40 12 289.05 1.21 90 32 66 42 263.45 0.32 91 32 67 43 263.44 0.32 92 32 141 123 190.34 0.42 93 33 40 11 289.13 1.25 94 33 41 12 288.70 1.18 95 33 42 13 287.24 1.49 96 33 43 14 276.17 3.95 97 33 52 23 263.62 0.35 98 33 54 25 270.32 2.31 99 33 59 30 288.93 1.19 100 33 64 39 287.51 1.73 101 33 65 40 277.12 0.86 102 33 66 41 263.54 0.30 103 33 106 83 263.60 0.33 104 34 38 8 289.29 1.24 105 34 39 9 289.18 1.27 106 34 40 10 289.14 1.26 107 34 41 11 289.04 1.22 108 34 64 38 287.77 1.62 109 34 65 39 287.12 1.52 110 34 67 41 287.98 1.67 111 34 70 44 289.19 1.29 112 34 73 47 289.22 1.29 113 35 38 7 289.28 1.26 114 35 39 8 289.22 1.28 115 35 41 10 289.18 1.26 116 35 60 31 289.18 1.26 117 35 63 36 289.12 1.27 118 35 64 37 288.88 1.22 119 36 37 5 289.50 1.27 120 36 38 6 289.39 1.28 121 36 62 34 289.17 1.26 122 36 63 35 289.14 1.26 123 36 65 37 289.14 1.27 124 36 82 54 289.16 1.27 125 36 84 56 289.11 1.28 126 37 37 3 294.08 1.01 127 37 37 4 289.50 1.27 128 37 39 6 289.47 1.28 129 38 65 31 289.12 1.27 130 40 73 37 318.71 6.21 131 40 141 111 190.85 0.44 132 40 151 121 191.24 0.35 133 40 193 167 173.61 0.21 134 41 64 27 315.70 5.24 135 42 195 167 176.81 0.20 136 43 54 11 390.36 0.60 137 43 195 166 176.72 0.15 138 43 196 167 176.94 0.14 139 43 197 168 182.60 2.27 140 44 52 8 368.09 0.06 141 44 53 9 386.62 1.27 142 44 54 10 390.36 0.60 143 44 196 166 176.84 0.12 144 44 197 167 182.62 2.27 145 45 52 7 386.62 1.27 146 45 53 8 389.56 2.71 147 45 121 86 215.79 0.51 148 45 198 167 187.96 0.28 149 45 209 178 189.06 0.49 150 46 49 3 386.62 1.27 151 46 51 5 386.63 1.27 152 46 52 6 394.92 2.88 153 46 68 26 482.49 1.34 154 46 108 68 477.67 1.98 155 46 112 76 311.62 0.56 156 46 118 82 216.28 0.40 157 46 119 83 216.15 0.46 158 46 120 84 215.86 0.49 159 46 121 85 215.84 0.49 160 47 51 4 461.42 5.01 161 47 120 83 215.88 0.48 162 47 121 84 215.86 0.49 163 47 123 86 215.22 0.69 164 47 238 205 62.77 0.07 165 48 120 82 216.08 0.49 166 49 111 72 401.89 1.52 167 49 112 73 357.88 2.44 168 49 120 81 216.06 0.50 169 51 241 204 43.30 1.31 170 51 242 205 20.97 0.29 171 53 209 170 189.28 0.58 172 53 212 173 188.04 0.30 173 53 238 199 62.63 0.01 174 54 196 156 177.54 0.24 175 54 212 172 188.30 0.35 176 55 58 3 475.22 2.67 177 55 196 155 187.80 0.34 178 55 212 171 188.93 0.51 179 57 195 152 188.89 0.49 180 57 214 171 188.87 0.50 181 58 195 151 188.03 0.32 182 68 118 56 216.16 0.35 183 69 117 54 216.17 0.36 184 69 118 55 216.18 0.36 185 71 141 76 190.37 0.43 186 71 154 89 189.91 0.23 187 71 155 90 188.91 0.54 188 72 141 75 190.38 0.42 189 72 153 87 190.69 0.43 190 73 141 74 190.39 0.42 191 73 151 84 190.96 0.35 192 73 152 85 190.96 0.35 193 73 153 86 190.75 0.46 194 74 153 85 190.97 0.35 195 75 153 84 190.76 0.47 196 79 118 45 216.24 0.35 197 81 118 43 216.22 0.38 198 89 237 158 65.33 0.10 199 89 241 162 36.00 6.24 200 90 237 157 67.07 0.71 201 91 234 153 100.99 0.29 202 91 237 156 67.08 0.71 203 97 175 86 203.32 0.87 204 97 175 85 203.33 0.87 205 97 172 81 203.22 0.86 206 97 175 84 203.33 0.88 207 97 215 126 189.36 0.55 208 97 217 128 189.06 0.49 209 98 175 83 203.21 0.93 210 98 180 88 202.79 0.81 211 98 215 125 189.28 0.55 212 99 180 87 201.97 1.22 213 99 214 123 189.30 0.54 214 99 215 124 189.10 0.49 215 100 177 83 202.98 0.99 216 100 180 86 197.94 0.35 217 101 179 84 197.94 0.35 218 101 234 141 101.58 0.23 219 102 214 120 188.35 0.32 220 102 229 135 120.45 0.14 221 103 212 117 188.99 0.53 222 103 229 134 120.45 0.14 223 103 234 139 99.69 0.47 224 103 237 142 67.08 0.71 225 103 238 143 64.96 0.01 226 104 237 141 65.60 0.03 227 105 237 140 65.31 0.11 228 105 238 141 62.93 0.15 229 105 241 144 23.48 0.02 230 105 242 145 21.71 0.13 231 112 118 6 216.59 0.29 232 113 118 5 216.97 0.13 233 114 118 4 216.97 0.13 234 115 118 3 233.94 5.08 235 115 119 4 256.50 16.37 236 121 200 83 188.91 0.51 237 121 207 90 189.05 0.49 238 121 208 91 188.96 0.52 239 121 209 92 188.82 0.55 240 122 206 88 189.31 0.57 241 122 207 89 189.20 0.56 242 122 208 90 188.97 0.52 243 122 209 91 188.94 0.52 244 123 208 89 189.20 0.56 245 123 209 90 189.00 0.52 246 123 231 112 101.53 0.04 247 123 235 116 80.25 0.35 248 123 238 119 64.21 0.45 249 124 208 88 189.28 0.58 250 124 209 89 189.26 0.57 251 124 210 90 188.97 0.52 252 124 231 111 101.77 0.13 253 124 232 112 100.84 0.19 254 124 235 115 88.13 0.64 255 125 128 3 266.72 13.87 256 125 232 111 101.55 0.04 257 125 235 114 91.94 1.79 258 126 235 113 98.22 0.29 259 126 236 114 98.19 0.28 260 127 232 109 101.78 0.14 261 127 233 110 101.59 0.04 262 128 203 79 295.61 3.42 263 128 232 108 102.24 0.36 264 129 203 78 298.29 2.08 265 129 210 85 226.56 0.74 266 129 230 105 120.00 0.04 267 129 232 107 101.75 0.12 268 130 134 4 321.74 0.05 269 130 162 32 325.77 1.94 270 130 201 75 295.37 3.36 271 130 203 77 304.68 1.11 272 130 210 84 270.44 15.70 273 131 134 3 331.89 1.24 274 132 162 30 333.32 1.96 275 132 163 31 339.30 4.91 276 132 164 32 339.29 4.92 277 132 165 33 339.40 4.95 278 132 181 51 339.30 4.91 279 133 161 28 339.38 4.85 280 133 162 29 339.35 4.90 281 134 161 27 342.54 3.93 282 134 162 28 339.57 4.91 283 135 159 24 441.63 20.64 284 135 160 25 427.52 13.87 285 135 161 26 347.81 1.29 286 136 159 23 441.66 20.64 287 136 160 24 441.57 20.65 288 136 162 26 427.41 13.86 289 136 199 67 370.18 1.04 290 136 200 68 422.74 0.09 291 137 159 22 475.88 3.54 292 137 199 66 412.41 5.13 293 138 189 55 334.37 0.28 294 138 190 56 319.47 0.91 295 138 198 64 409.11 1.80 296 138 228 94 120.72 0.27 297 140 194 58 337.81 0.07 298 141 194 57 338.68 0.14 299 142 192 54 338.09 0.14 300 142 193 55 338.10 0.14 301 142 194 56 338.13 0.14 302 143 191 52 337.78 0.14 303 143 192 53 338.16 0.12 304 146 220 77 337.66 0.10 305 151 192 45 340.68 1.14 306 151 193 46 340.69 1.13 307 158 188 34 471.16 3.25 308 159 188 33 476.95 0.50 309 160 188 32 477.19 0.40 310 160 189 33 471.54 3.12 311 163 225 66 122.81 0.36 312 168 225 61 128.48 3.19 313 170 223 55 155.47 2.95 314 170 224 56 151.84 1.09 315 171 223 54 144.02 0.53 316 171 224 55 139.14 1.71 317 171 225 56 139.05 1.66 318 172 224 54 139.14 1.71 319 172 225 55 138.85 1.57 320 172 227 57 133.91 1.01 321 176 227 53 122.81 0.36 322 178 230 54 122.70 0.35 323 179 229 52 122.62 0.35 324 179 230 53 120.79 0.03 325 179 233 56 114.04 0.85 326 179 234 57 109.02 1.66 327 180 227 49 122.72 0.35 328 180 228 50 122.63 0.36 329 180 230 52 120.78 0.03 330 181 227 48 122.72 0.35 331 181 228 49 122.58 0.30 332 181 230 51 120.43 0.14 333 182 225 45 122.81 0.36 334 182 226 46 122.77 0.35 335 182 227 47 122.70 0.35 336 183 225 44 122.81 0.36 337 183 226 45 122.73 0.35 338 183 228 47 122.66 0.36 339 184 225 43 122.81 0.36 340 186 221 34 317.28 47.89 341 186 222 35 286.09 63.48 342 186 223 36 140.38 1.29 343 186 223 37 140.57 1.08 344 186 224 38 139.19 0.71 345 186 225 39 124.99 0.90 346 189 221 31 436.75 11.35 347 189 226 37 122.78 0.35 348 190 194 4 437.25 3.79 349 190 213 23 376.17 7.25 350 190 228 38 122.75 0.35 351 191 194 3 358.98 0.39 352 194 197 3 351.68 0.69 353 199 211 12 383.95 2.81 354 199 228 29 120.45 0.14 355 201 210 9 378.98 0.54 356 209 231 22 101.54 0.04 357 210 231 21 101.56 0.04 358 211 228 17 120.45 0.14 359 211 229 18 120.06 0.00 360 211 231 20 101.56 0.03 361 212 228 16 120.45 0.14 362 212 229 17 120.17 0.04 363 212 231 19 101.77 0.14 364 213 228 15 120.47 0.14 365 214 227 13 122.72 0.35 366 214 228 14 121.92 0.55 367 214 229 15 120.50 0.13 368 215 226 11 122.81 0.36 369 215 227 12 122.75 0.35 370 217 222 4 346.16 1.79 371 217 224 7 134.44 0.81 372 219 222 3 395.26 0.18 373 222 224 3 299.48 3.88 374 229 234 5 273.28 18.07 375 230 233 3 314.72 2.01 376 230 234 4 312.75 1.65 377 231 234 3 312.75 1.65 378 231 235 4 273.29 18.07 379 231 238 7 142.24 38.37 380 232 235 3 314.69 1.99 381 234 237 3 301.83 3.56 382 234 238 4 232.24 1.06 383 235 238 3 283.62 7.09 384 235 239 4 232.24 1.06 385 236 239 3 276.69 14.04 386 236 240 4 264.06 13.94 387 237 240 3 310.23 1.24 388 237 241 4 264.07 13.94 389 238 241 3 313.20 0.25 390 238 242 4 264.69 13.62 391 239 242 3 303.65 0.23 392 239 243 4 264.69 13.62 393 240 243 3 313.81 2.93