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 16 142 140 37.02 0.29 2 16 143 141 45.13 0.40 3 16 144 142 47.41 0.29 4 16 156 154 37.30 0.42 5 16 157 155 37.29 0.42 6 16 158 156 41.45 0.66 7 16 189 191 45.33 0.02 8 16 190 192 36.97 0.26 9 16 194 196 36.84 0.32 10 17 143 140 47.41 0.29 11 17 144 141 47.41 0.29 12 17 145 142 47.71 0.34 13 17 146 143 50.94 0.11 14 17 188 189 46.74 0.29 15 17 189 190 46.23 0.32 16 17 191 192 46.22 0.33 17 17 220 220 46.26 0.34 18 17 221 221 46.28 0.33 19 18 156 152 53.37 0.09 20 18 188 188 47.40 0.32 21 19 157 152 50.23 1.43 22 19 158 153 47.43 0.31 23 19 188 187 47.88 0.26 24 20 156 150 78.90 0.13 25 20 157 151 56.71 0.85 26 21 144 137 84.94 0.66 27 21 152 145 86.28 0.96 28 21 154 147 86.38 0.96 29 21 155 148 85.12 0.57 30 21 156 149 83.09 0.30 31 22 26 4 296.73 1.55 32 22 27 5 289.88 2.67 33 22 139 131 85.12 0.57 34 22 154 146 96.62 1.61 35 22 155 147 86.25 1.01 36 22 156 148 85.11 0.57 37 22 157 149 84.83 0.60 38 23 26 3 313.33 1.68 39 23 27 4 294.43 0.40 40 23 71 56 156.29 28.21 41 23 154 145 96.87 1.50 42 24 27 3 291.90 1.66 43 24 28 4 289.88 2.67 44 24 30 6 273.82 4.33 45 24 69 53 172.09 20.32 46 24 70 54 171.54 21.53 47 24 71 55 168.19 23.21 48 24 117 107 167.13 1.10 49 24 155 145 96.91 1.52 50 25 28 3 295.63 0.21 51 25 116 105 189.52 0.41 52 25 117 106 185.12 0.40 53 27 30 3 300.63 2.13 54 27 137 124 147.00 0.10 55 27 139 126 139.54 1.69 56 27 155 142 182.42 0.04 57 27 157 144 143.43 1.77 58 28 117 103 190.74 0.24 59 28 118 104 190.31 0.12 60 28 119 105 189.73 0.33 61 29 45 20 224.25 17.93 62 29 46 21 207.82 9.79 63 29 119 104 190.53 0.14 64 29 120 105 189.72 0.33 65 29 121 106 189.52 0.42 66 29 137 122 188.53 0.07 67 29 198 187 177.63 0.26 68 29 200 189 188.81 0.20 69 29 207 196 190.27 0.24 70 30 40 14 236.25 21.87 71 30 43 17 227.03 18.60 72 30 44 18 226.24 18.82 73 30 68 46 229.74 17.10 74 30 139 123 188.72 0.01 75 30 140 124 190.16 0.09 76 30 141 125 190.96 0.24 77 30 155 139 191.07 0.16 78 30 198 186 183.99 1.35 79 31 43 16 227.03 18.60 80 31 44 17 226.24 18.83 81 31 45 18 227.06 18.41 82 31 52 25 226.95 18.43 83 31 66 43 229.75 17.09 84 31 67 44 229.75 17.10 85 31 68 45 229.74 17.10 86 32 40 12 236.25 21.86 87 32 66 42 229.82 17.12 88 32 67 43 229.90 17.17 89 32 141 123 191.30 0.28 90 33 40 11 236.25 21.87 91 33 41 12 236.03 21.89 92 33 42 13 235.19 22.18 93 33 43 14 233.47 21.01 94 33 44 15 233.47 20.74 95 33 54 25 233.00 20.97 96 33 59 30 235.92 21.96 97 33 64 39 236.06 20.23 98 33 65 40 233.57 18.99 99 33 66 41 231.49 17.96 100 33 106 83 231.66 19.59 101 34 38 8 237.03 21.60 102 34 39 9 236.68 21.77 103 34 40 10 236.31 21.87 104 34 41 11 236.17 21.82 105 34 64 38 237.65 21.01 106 34 65 39 234.74 19.55 107 34 67 41 237.33 20.80 108 34 70 44 238.25 20.92 109 34 73 47 238.18 20.98 110 35 38 7 237.94 21.16 111 35 39 8 236.83 21.69 112 35 41 10 236.37 21.84 113 35 60 31 237.76 21.12 114 35 63 36 237.74 21.04 115 35 64 37 237.71 21.04 116 36 38 6 237.96 21.16 117 36 62 34 237.81 21.04 118 36 63 35 237.75 21.04 119 36 65 37 237.78 21.00 120 36 84 56 237.79 21.00 121 37 37 3 307.33 3.08 122 37 37 4 238.04 21.17 123 37 39 6 238.02 21.18 124 38 65 31 254.25 12.77 125 40 73 37 313.94 14.23 126 40 141 111 192.91 0.33 127 40 151 121 192.86 0.24 128 40 193 167 174.00 0.54 129 41 64 27 318.75 2.68 130 42 195 167 196.13 9.56 131 42 196 168 205.13 8.28 132 43 54 11 386.84 1.33 133 43 195 166 200.95 11.98 134 43 196 167 206.56 9.70 135 43 197 168 205.34 8.12 136 44 52 8 364.06 0.96 137 44 53 9 383.91 0.12 138 44 54 10 386.84 1.33 139 44 196 166 202.83 12.92 140 44 197 167 207.90 10.38 141 44 198 168 209.97 9.28 142 45 52 7 383.90 0.12 143 45 53 8 394.81 1.73 144 45 121 86 213.53 8.30 145 45 198 167 210.03 9.32 146 45 209 178 211.33 8.71 147 46 51 5 383.93 0.12 148 46 52 6 394.64 1.81 149 46 68 26 480.75 1.65 150 46 108 68 487.98 0.41 151 46 112 76 299.53 2.73 152 46 118 82 214.09 8.47 153 46 119 83 214.09 8.47 154 46 120 84 213.78 8.42 155 46 121 85 213.68 8.37 156 47 51 4 451.31 0.09 157 47 120 83 213.94 8.44 158 47 121 84 213.74 8.37 159 47 123 86 213.37 8.53 160 47 238 205 64.27 0.60 161 48 120 82 214.12 8.46 162 49 111 72 411.49 1.50 163 49 112 73 346.13 3.49 164 49 120 81 214.12 8.46 165 51 241 204 45.54 2.42 166 51 242 205 23.86 0.44 167 53 209 170 211.96 8.96 168 53 212 173 210.36 9.52 169 53 238 199 63.98 0.46 170 54 196 156 202.90 12.89 171 54 212 172 210.23 9.42 172 55 58 3 460.42 2.23 173 55 196 155 208.75 10.03 174 55 212 171 210.36 9.35 175 57 195 152 210.11 9.35 176 57 214 171 210.09 9.35 177 58 195 151 209.42 9.62 178 58 196 152 210.05 9.33 179 68 118 56 217.44 10.67 180 69 117 54 215.25 11.93 181 69 118 55 215.02 11.87 182 71 141 76 214.87 11.72 183 71 154 89 214.81 11.71 184 71 155 90 213.90 11.78 185 72 141 75 215.03 11.65 186 72 153 87 215.03 11.65 187 72 154 88 214.85 11.73 188 73 141 74 215.09 11.62 189 73 151 84 215.09 11.62 190 73 152 85 215.09 11.62 191 73 153 86 215.09 11.62 192 74 153 85 215.10 11.61 193 79 118 45 218.17 10.52 194 81 118 43 218.12 10.49 195 89 237 158 66.78 0.49 196 89 241 162 45.51 2.56 197 90 237 157 67.53 0.87 198 91 234 153 97.44 1.11 199 91 237 156 67.53 0.87 200 97 172 81 212.23 8.81 201 97 175 84 212.31 8.79 202 97 215 126 211.40 9.05 203 97 217 128 210.44 9.44 204 98 175 83 212.28 8.80 205 98 180 88 212.40 8.81 206 98 215 125 211.22 9.10 207 99 180 87 212.40 8.80 208 99 214 123 211.52 8.96 209 99 215 124 211.13 9.12 210 100 177 83 212.28 8.80 211 100 180 86 212.23 8.83 212 101 234 141 97.93 1.29 213 102 214 120 210.21 9.40 214 102 229 135 118.09 1.32 215 103 212 117 211.09 9.09 216 103 229 134 117.69 1.52 217 103 234 139 94.39 0.56 218 103 237 142 66.77 0.49 219 103 238 143 66.23 0.26 220 104 237 141 66.78 0.49 221 105 237 140 66.77 0.50 222 105 238 141 64.17 0.47 223 105 241 144 24.32 0.23 224 105 242 145 24.03 0.36 225 112 118 6 218.09 10.16 226 114 118 4 218.66 10.11 227 115 118 3 284.28 0.57 228 115 119 4 242.14 21.63 229 121 200 83 217.31 11.22 230 121 207 90 217.47 11.27 231 121 208 91 217.38 11.23 232 121 209 92 217.25 11.25 233 122 207 89 217.50 11.27 234 122 208 90 217.41 11.25 235 122 209 91 217.45 11.27 236 123 208 89 217.56 11.30 237 123 209 90 217.49 11.28 238 123 231 112 97.42 1.02 239 123 235 116 79.04 0.24 240 123 238 119 65.19 0.91 241 124 128 4 227.22 14.67 242 124 208 88 217.62 11.30 243 124 209 89 217.61 11.30 244 124 231 111 97.48 1.02 245 124 232 112 97.29 1.05 246 124 235 115 85.88 2.25 247 125 128 3 275.35 5.32 248 125 232 111 97.46 1.03 249 125 235 114 94.39 0.56 250 126 235 113 96.73 1.15 251 126 236 114 95.50 0.73 252 127 232 109 97.49 1.04 253 127 233 110 97.48 1.04 254 128 203 79 304.80 2.24 255 128 204 80 312.63 1.62 256 129 203 78 304.85 2.25 257 129 210 85 290.83 1.09 258 129 230 105 117.42 1.52 259 129 232 107 98.62 0.48 260 130 134 4 316.30 0.03 261 130 162 32 326.75 5.19 262 130 201 75 304.37 2.29 263 130 203 77 306.13 1.64 264 130 210 84 304.00 2.37 265 131 134 3 335.85 2.98 266 132 162 30 330.75 6.13 267 132 163 31 330.84 6.19 268 132 164 32 330.94 6.24 269 132 999 33 330.96 6.23 270 132 181 51 330.96 6.27 271 133 161 28 336.81 7.08 272 133 162 29 334.95 7.99 273 134 161 27 344.33 3.38 274 134 162 28 337.46 6.77 275 135 159 24 465.32 8.51 276 135 160 25 462.99 7.56 277 135 161 26 345.43 2.85 278 136 159 23 482.91 0.29 279 136 160 24 465.16 8.54 280 136 162 26 415.67 30.91 281 136 199 67 374.81 1.98 282 136 200 68 426.24 4.86 283 137 159 22 485.38 0.94 284 137 198 65 386.78 0.45 285 137 199 66 404.55 0.74 286 138 190 56 320.55 1.84 287 138 198 64 401.59 1.96 288 138 213 79 342.91 0.18 289 138 228 94 118.09 1.32 290 140 194 58 337.60 2.56 291 141 194 57 343.17 0.10 292 142 192 54 343.03 0.14 293 142 193 55 343.05 0.14 294 142 194 56 343.10 0.13 295 143 191 52 342.71 0.22 296 143 192 53 343.24 0.03 297 146 220 77 337.60 2.72 298 151 192 45 355.38 5.92 299 151 193 46 364.47 1.39 300 158 188 34 457.70 0.48 301 159 188 33 457.97 0.40 302 160 188 32 476.63 4.46 303 162 201 43 484.05 1.61 304 163 225 66 121.53 1.81 305 168 225 61 184.22 28.98 306 170 223 55 196.47 23.34 307 170 224 56 196.41 23.37 308 171 223 54 189.58 26.78 309 171 224 55 189.48 26.76 310 171 225 56 189.45 26.75 311 172 224 54 189.47 26.78 312 172 225 55 189.35 26.81 313 172 227 57 186.21 28.34 314 176 227 53 121.33 1.71 315 178 230 54 120.92 1.79 316 179 230 53 118.81 0.96 317 179 234 57 109.60 0.67 318 180 227 49 121.19 1.71 319 180 228 50 121.08 1.72 320 180 230 52 118.39 1.16 321 181 227 48 121.11 1.71 322 181 228 49 120.95 1.65 323 181 230 51 118.63 1.04 324 182 225 45 121.53 1.79 325 182 226 46 121.30 1.73 326 182 227 47 121.09 1.71 327 183 225 44 121.52 1.80 328 183 226 45 121.27 1.75 329 183 228 47 121.09 1.71 330 184 225 43 121.52 1.80 331 186 221 34 209.36 29.59 332 186 222 35 209.34 29.59 333 186 223 36 196.77 23.32 334 186 223 37 191.24 26.08 335 186 224 38 189.42 26.84 336 186 225 39 185.38 28.82 337 189 221 31 366.63 0.39 338 189 226 37 121.51 1.79 339 190 194 4 446.21 1.78 340 190 213 23 380.18 3.42 341 190 228 38 121.24 1.70 342 191 194 3 368.06 0.49 343 194 197 3 348.00 0.74 344 197 213 16 487.78 0.30 345 199 211 12 388.91 0.02 346 199 228 29 117.70 1.51 347 201 210 9 380.42 4.47 348 209 231 22 97.43 1.02 349 210 231 21 97.44 1.02 350 211 228 17 117.69 1.51 351 211 229 18 117.41 1.42 352 211 231 20 97.44 1.02 353 212 228 16 117.70 1.51 354 212 229 17 117.35 1.45 355 212 231 19 97.48 1.04 356 213 228 15 118.03 1.35 357 214 227 13 121.19 1.71 358 214 228 14 119.86 2.17 359 214 229 15 118.10 1.32 360 215 226 11 121.51 1.79 361 215 227 12 121.25 1.73 362 217 222 4 355.30 2.79 363 217 224 7 187.01 27.91 364 219 222 3 392.82 2.38 365 222 224 3 298.68 1.53 366 229 234 5 296.75 2.94 367 230 233 3 318.03 3.67 368 230 234 4 300.72 4.91 369 231 234 3 309.19 0.68 370 231 235 4 300.73 4.91 371 231 238 7 168.87 51.57 372 232 235 3 314.45 0.64 373 234 237 3 299.08 2.19 374 234 238 4 250.53 12.89 375 235 238 3 287.06 0.15 376 235 239 4 250.63 12.94 377 236 239 3 290.78 3.51 378 236 240 4 251.21 13.22 379 237 240 3 302.50 2.35 380 237 241 4 285.24 3.10 381 238 241 3 310.46 1.62 382 238 242 4 251.96 13.54 383 239 242 3 299.32 3.95 384 239 243 4 252.18 13.66 385 240 243 3 323.16 5.48