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 54.78 0.68 2 18 46 28 54.68 0.73 3 18 47 29 54.68 0.73 4 18 48 30 48.77 1.64 5 18 49 31 51.66 0.10 6 18 53 35 37.23 0.93 7 19 46 27 54.90 0.70 8 19 47 28 54.90 0.70 9 20 47 27 55.23 0.62 10 20 48 28 55.03 0.64 11 20 60 40 54.96 0.67 12 20 65 45 55.88 0.57 13 20 70 50 54.89 0.70 14 20 71 51 55.02 0.64 15 20 72 52 55.03 0.64 16 21 24 3 367.61 1.27 17 21 25 4 190.53 32.38 18 21 47 26 56.18 0.56 19 21 71 50 55.16 0.65 20 22 26 4 124.50 1.73 21 22 69 47 55.94 0.58 22 22 70 48 56.05 0.54 23 22 71 49 56.18 0.56 24 23 26 3 327.22 0.61 25 23 35 12 57.23 0.98 26 23 37 14 57.52 0.84 27 23 69 46 57.11 1.03 28 23 71 48 57.23 0.98 29 23 101 78 59.09 1.09 30 23 104 81 59.12 1.11 31 23 105 82 58.30 1.30 32 23 108 85 58.76 1.28 33 24 71 47 58.34 1.29 34 24 101 77 59.13 1.11 35 24 104 80 59.37 1.23 36 24 108 84 84.58 13.84 37 26 69 43 59.01 1.08 38 26 108 82 174.98 27.55 39 27 30 3 351.49 5.11 40 27 31 4 334.06 11.04 41 27 69 42 525.78 3.59 42 28 31 3 367.94 0.02 43 28 108 80 178.16 26.16 44 32 112 80 447.31 0.94 45 33 112 79 447.31 0.94 46 33 113 80 447.31 0.94 47 33 211 178 30.64 0.12 48 34 113 79 447.31 0.93 49 34 115 81 447.30 0.93 50 34 207 173 74.04 0.76 51 34 211 177 30.64 0.12 52 35 112 77 527.60 4.25 53 35 113 78 450.26 1.39 54 35 114 79 447.33 0.93 55 35 115 80 447.32 0.93 56 36 115 79 447.33 0.93 57 36 116 80 447.31 0.93 58 36 117 81 447.31 0.93 59 36 203 167 93.14 0.88 60 37 115 78 448.81 1.47 61 37 116 79 447.32 0.93 62 37 117 80 447.32 0.93 63 38 117 79 447.33 0.93 64 38 118 80 447.32 0.93 65 38 119 81 447.32 0.93 66 39 117 78 448.13 1.22 67 39 118 79 447.31 0.93 68 39 119 80 447.32 0.93 69 39 122 83 354.95 0.07 70 39 125 86 354.72 0.04 71 40 119 79 447.33 0.93 72 40 122 82 355.00 0.06 73 41 119 78 447.38 0.93 74 41 120 79 447.32 0.93 75 42 121 79 447.31 0.93 76 44 119 75 448.26 1.28 77 51 119 68 447.33 0.93 78 51 147 96 304.44 0.49 79 51 191 140 102.62 0.64 80 51 192 141 101.24 0.10 81 51 195 144 98.37 0.15 82 54 195 141 98.38 0.15 83 54 196 142 98.37 0.16 84 55 147 92 304.44 0.49 85 55 195 140 98.39 0.16 86 55 200 145 98.12 0.18 87 55 203 148 97.74 0.33 88 58 196 138 98.39 0.17 89 58 200 142 98.23 0.13 90 59 115 56 447.45 0.91 91 59 203 144 92.70 1.09 92 59 204 145 91.49 0.92 93 62 204 142 91.61 0.87 94 62 208 146 76.20 0.12 95 63 204 141 91.61 0.87 96 63 207 144 76.32 0.05 97 73 125 52 354.72 0.04 98 77 121 44 447.23 0.95 99 77 122 45 435.72 3.98 100 77 125 48 354.78 0.07 101 79 121 42 447.27 0.93 102 80 121 41 448.14 1.28 103 83 121 38 447.45 0.92 104 84 121 37 447.67 1.02 105 84 182 98 154.84 4.37 106 87 151 64 299.94 3.07 107 88 124 36 417.98 8.27 108 88 128 40 354.82 0.07 109 88 131 43 354.73 0.03 110 88 132 44 354.61 0.03 111 88 151 63 284.24 1.57 112 89 121 32 447.34 0.93 113 89 124 35 382.01 1.71 114 89 151 62 284.28 1.58 115 90 121 31 447.31 0.93 116 90 125 35 355.08 0.01 117 94 125 31 354.76 0.06 118 95 125 30 354.76 0.06 119 95 128 33 347.01 3.21 120 95 129 34 320.13 0.70 121 98 116 18 451.21 1.74 122 98 125 27 354.75 0.06 123 98 126 28 354.57 0.04 124 98 129 31 320.11 0.70 125 99 129 30 320.08 0.71 126 99 132 33 317.81 0.64 127 99 133 34 307.49 0.27 128 102 114 12 502.47 3.19 129 102 116 14 447.34 0.93 130 102 129 27 320.05 0.69 131 102 130 28 319.94 0.69 132 102 133 31 307.48 0.27 133 102 137 35 307.31 0.29 134 102 141 39 307.16 0.29 135 103 133 30 307.49 0.27 136 103 137 34 307.19 0.30 137 105 114 9 450.34 1.42 138 106 137 31 307.16 0.29 139 106 140 34 307.16 0.29 140 109 112 3 447.31 0.94 141 110 140 30 307.14 0.30 142 111 211 100 30.73 0.08 143 113 140 27 307.16 0.29 144 113 142 29 306.95 0.29 145 113 207 94 74.72 0.43 146 113 210 97 32.66 0.88 147 113 211 98 28.34 1.04 148 114 137 23 307.33 0.28 149 114 140 26 307.17 0.30 150 114 141 27 307.07 0.29 151 114 142 28 307.07 0.29 152 115 141 26 307.17 0.29 153 115 142 27 307.12 0.30 154 115 143 28 306.93 0.30 155 115 203 88 93.19 0.90 156 115 207 92 75.98 0.21 157 116 130 14 319.79 0.59 158 116 141 25 307.22 0.30 159 116 143 27 307.13 0.31 160 116 144 28 306.38 0.10 161 116 145 29 306.25 0.15 162 116 203 87 95.11 0.03 163 117 144 27 307.01 0.29 164 117 145 28 306.35 0.10 165 118 122 4 355.25 0.07 166 118 123 5 354.92 0.07 167 118 145 27 307.00 0.29 168 118 146 28 306.28 0.12 169 118 147 29 305.93 0.24 170 119 122 3 364.36 2.62 171 119 123 4 355.00 0.06 172 119 147 28 304.44 0.49 173 119 188 69 111.62 2.54 174 119 189 70 107.45 0.48 175 119 191 72 101.63 0.07 176 120 123 3 368.19 0.68 177 120 124 4 364.03 0.37 178 120 147 27 306.75 0.21 179 120 148 28 304.46 0.47 180 120 150 30 291.23 1.30 181 120 188 68 111.62 2.54 182 121 124 3 365.78 0.51 183 121 125 4 361.19 1.02 184 121 150 29 291.19 1.29 185 122 125 3 361.23 1.03 186 122 126 4 355.66 0.18 187 123 126 3 357.09 0.89 188 123 127 4 355.55 0.12 189 123 146 23 306.93 0.28 190 123 147 24 306.74 0.21 191 123 149 26 291.19 1.29 192 124 127 3 359.36 1.98 193 124 128 4 355.25 0.04 194 124 149 25 295.57 0.90 195 124 150 26 284.28 1.58 196 124 151 27 282.50 0.76 197 125 128 3 355.26 0.04 198 125 129 4 355.25 0.04 199 126 129 3 360.11 2.27 200 126 130 4 347.81 3.87 201 126 146 20 306.99 0.28 202 127 130 3 360.19 2.25 203 127 131 4 355.57 0.01 204 127 149 22 297.54 1.89 205 127 159 32 213.78 0.57 206 128 131 3 362.65 3.34 207 128 132 4 355.57 0.01 208 129 132 3 361.80 2.26 209 129 133 4 355.56 0.03 210 130 133 3 361.25 2.54 211 130 138 8 307.44 0.31 212 130 141 11 307.32 0.29 213 130 144 14 307.16 0.29 214 130 159 29 213.78 0.57 215 130 162 32 213.52 0.49 216 131 138 7 308.05 0.41 217 131 160 29 213.71 0.57 218 131 161 30 213.63 0.54 219 133 137 4 356.45 0.15 220 133 138 5 326.81 3.45 221 133 141 8 309.28 0.29 222 134 137 3 361.85 2.43 223 134 138 4 359.89 1.57 224 135 138 3 360.63 1.20 225 135 139 4 357.19 0.53 226 136 139 3 370.42 3.69 227 136 140 4 359.61 1.73 228 137 140 3 366.53 0.34 229 137 141 4 363.13 1.30 230 138 141 3 364.30 1.45 231 138 161 23 213.59 0.51 232 138 162 24 213.47 0.52 233 139 166 27 212.86 0.69 234 141 144 3 419.04 1.15 235 141 162 21 213.53 0.48 236 141 166 25 212.22 1.00 237 142 166 24 212.19 0.99 238 142 206 64 80.78 0.32 239 142 207 65 76.36 0.02 240 142 210 68 68.55 1.70 241 143 162 19 213.62 0.51 242 143 166 23 212.19 0.99 243 143 202 59 98.25 0.14 244 143 203 60 96.96 0.74 245 143 206 63 80.78 0.32 246 144 159 15 213.77 0.56 247 144 162 18 213.58 0.48 248 144 166 22 212.28 0.97 249 144 167 23 212.17 1.01 250 144 168 24 212.13 1.00 251 144 202 58 98.31 0.17 252 144 203 59 97.05 0.71 253 145 168 23 212.12 1.01 254 145 170 25 211.97 1.01 255 145 199 54 98.39 0.16 256 145 202 57 98.39 0.20 257 145 203 58 97.95 0.29 258 146 149 3 367.82 2.52 259 146 159 13 213.80 0.57 260 146 167 21 212.28 0.97 261 146 168 22 212.20 1.00 262 146 169 23 211.98 1.02 263 146 170 24 211.31 1.32 264 147 170 23 211.29 1.32 265 147 191 44 102.75 0.61 266 147 194 47 101.42 0.12 267 147 195 48 101.42 0.12 268 147 199 52 101.23 0.08 269 148 170 22 212.12 1.02 270 148 171 23 211.29 1.33 271 148 175 27 211.22 1.35 272 148 177 29 211.05 1.29 273 148 178 30 209.12 0.85 274 148 188 40 107.47 0.47 275 148 191 43 106.98 0.35 276 149 152 3 346.04 8.52 277 149 155 6 286.24 17.82 278 149 157 8 214.04 0.56 279 149 158 9 214.04 0.56 280 149 169 20 212.19 1.01 281 149 171 22 212.03 0.98 282 149 178 29 205.21 0.30 283 150 154 4 376.20 0.58 284 150 177 27 209.84 1.20 285 150 182 32 163.05 0.28 286 151 154 3 363.15 0.13 287 151 155 4 339.98 9.88 288 152 155 3 362.19 0.61 289 152 156 4 321.17 0.45 290 152 157 5 214.25 0.62 291 152 169 17 212.86 0.74 292 152 171 19 212.38 0.95 293 152 178 26 208.31 0.45 294 153 156 3 363.62 5.72 295 153 178 25 211.31 1.17 296 153 179 26 205.28 0.33 297 153 180 27 204.86 0.44 298 154 180 26 204.88 0.47 299 155 158 3 366.83 1.68 300 155 160 5 265.20 24.56 301 157 169 12 212.89 0.72 302 158 162 4 345.58 7.43 303 158 163 5 275.12 19.77 304 158 164 6 213.64 0.52 305 159 162 3 361.09 0.33 306 159 167 8 213.01 0.68 307 162 166 4 366.28 2.67 308 162 167 5 325.72 1.37 309 163 166 3 371.05 1.99 310 163 167 4 342.38 6.95 311 164 167 3 365.23 2.77 312 165 202 37 98.44 0.18 313 165 206 41 96.75 0.84 314 166 202 36 98.39 0.20 315 166 206 40 92.48 1.09 316 167 202 35 98.41 0.20 317 168 202 34 98.43 0.20 318 170 191 21 106.78 0.23 319 170 194 24 101.43 0.12 320 170 198 28 101.33 0.08 321 170 199 29 101.33 0.08 322 171 191 20 111.42 2.35 323 172 187 15 113.95 1.69 324 172 190 18 113.59 1.60 325 172 191 19 112.50 1.96 326 173 187 14 122.64 0.86 327 174 185 11 136.15 0.31 328 174 187 13 122.23 0.65 329 175 187 12 122.21 0.64 330 175 188 13 115.81 2.54 331 175 191 16 115.80 2.54 332 176 181 5 479.37 12.59 333 176 183 7 358.86 2.44 334 176 185 9 131.47 2.85 335 177 181 4 392.94 1.41 336 177 182 5 358.86 2.44 337 177 183 6 325.52 0.59 338 177 188 11 119.38 0.72 339 178 191 13 115.69 2.56 340 184 188 4 334.43 0.73 341 184 189 5 347.12 4.76 342 185 188 3 366.98 2.14 343 186 189 3 367.35 1.96 344 186 190 4 366.95 2.16 345 187 190 3 367.08 2.20 346 187 191 4 374.05 1.28 347 188 191 3 403.54 3.27 348 190 193 3 411.89 2.46 349 191 194 3 374.22 0.33 350 191 195 4 339.53 2.80 351 192 195 3 363.13 0.47 352 192 196 4 339.53 2.81 353 193 196 3 355.05 8.86 354 193 197 4 335.07 1.12 355 193 198 5 335.06 1.14 356 194 197 3 367.06 2.85 357 194 198 4 331.15 0.76 358 194 199 5 283.93 19.79 359 194 200 6 324.86 6.20 360 195 199 4 283.92 19.79 361 195 200 5 324.87 6.20 362 196 200 4 337.37 0.49 363 197 200 3 371.44 0.37 364 197 201 4 337.38 0.49 365 198 201 3 349.16 4.49 366 198 202 4 337.36 0.48 367 199 202 3 358.41 0.14 368 199 203 4 332.00 2.79 369 200 203 3 360.31 0.82 370 200 204 4 331.06 3.24 371 201 204 3 348.28 8.06 372 201 205 4 331.09 3.25 373 202 205 3 366.06 2.70 374 202 206 4 350.69 6.83 375 203 206 3 354.04 8.71 376 203 207 4 349.98 7.19 377 204 207 3 356.36 7.55 378 204 208 4 348.16 8.10 379 205 208 3 349.99 7.19 380 205 209 4 348.07 8.05 381 206 209 3 382.57 1.95 382 206 210 4 345.62 9.28 383 207 210 3 366.17 0.98 384 207 211 4 329.51 1.22 385 208 211 3 353.13 7.50