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 61.20 0.10 2 18 46 28 61.23 0.11 3 18 47 29 61.22 0.12 4 18 48 30 48.91 2.23 5 18 49 31 53.70 0.03 6 18 53 35 41.75 0.74 7 19 46 27 61.50 0.03 8 19 47 28 61.30 0.07 9 20 47 27 62.20 0.14 10 20 48 28 61.61 0.07 11 20 60 40 61.41 0.13 12 20 70 50 61.22 0.10 13 20 71 51 61.63 0.18 14 20 72 52 61.84 0.07 15 21 24 3 348.30 3.94 16 21 25 4 280.64 28.94 17 21 47 26 63.17 0.04 18 21 71 50 61.92 0.04 19 22 25 3 348.37 4.12 20 22 26 4 242.65 47.94 21 22 69 47 62.48 0.14 22 22 70 48 62.98 0.03 23 22 71 49 63.02 0.04 24 23 26 3 352.35 6.91 25 23 35 12 63.08 0.07 26 23 37 14 63.45 0.10 27 23 69 46 63.08 0.07 28 23 71 48 63.23 0.01 29 23 101 78 66.40 0.42 30 23 104 81 66.67 0.32 31 23 105 82 65.19 0.59 32 23 108 85 66.72 0.29 33 24 71 47 63.81 0.21 34 24 101 77 66.32 0.42 35 24 104 80 66.70 0.29 36 24 108 84 97.11 15.49 37 26 69 43 65.97 0.34 38 26 108 82 132.31 1.28 39 27 30 3 354.30 5.77 40 27 31 4 347.30 3.77 41 27 69 42 534.16 2.88 42 28 31 3 365.81 0.39 43 28 108 80 187.31 21.75 44 32 112 80 451.57 0.18 45 33 112 79 451.57 0.18 46 33 113 80 451.56 0.18 47 33 211 178 36.49 0.07 48 34 113 79 451.57 0.18 49 34 115 81 451.56 0.18 50 34 207 173 80.03 0.67 51 34 211 177 36.41 0.00 52 35 112 77 534.63 1.30 53 35 113 78 457.92 1.80 54 35 114 79 451.57 0.18 55 35 115 80 451.57 0.18 56 36 115 79 451.57 0.18 57 36 116 80 451.57 0.18 58 36 117 81 451.57 0.18 59 36 203 167 102.70 0.72 60 37 115 78 451.91 0.24 61 37 116 79 451.57 0.18 62 37 117 80 451.57 0.18 63 38 117 79 451.58 0.18 64 38 118 80 451.57 0.18 65 38 119 81 451.57 0.18 66 39 117 78 451.85 0.27 67 39 118 79 451.56 0.19 68 39 119 80 451.56 0.19 69 39 122 83 359.43 2.76 70 39 125 86 358.97 2.99 71 40 119 79 451.57 0.18 72 40 122 82 359.55 2.79 73 41 119 78 451.72 0.24 74 41 120 79 451.56 0.20 75 44 119 75 451.99 0.28 76 51 119 68 451.56 0.18 77 51 147 96 306.93 0.67 78 51 191 140 115.84 1.33 79 51 192 141 115.34 1.38 80 51 195 144 109.73 0.52 81 54 195 141 109.72 0.51 82 54 196 142 109.67 0.49 83 55 147 92 307.19 0.53 84 55 195 140 109.68 0.49 85 55 200 145 109.02 0.45 86 55 203 148 107.02 0.58 87 58 196 138 109.67 0.49 88 58 200 142 108.88 0.52 89 58 204 146 102.89 0.82 90 59 115 56 451.73 0.23 91 59 203 144 102.89 0.82 92 59 204 145 102.26 0.75 93 62 204 142 102.09 0.83 94 62 208 146 85.44 2.00 95 63 204 141 101.99 0.89 96 63 207 144 85.46 1.99 97 73 125 52 358.44 3.27 98 77 121 44 451.49 0.19 99 77 122 45 433.48 3.10 100 77 125 48 359.14 3.03 101 80 121 41 451.80 0.28 102 83 121 38 451.80 0.28 103 84 121 37 451.63 0.26 104 84 182 98 154.26 2.96 105 85 182 97 174.33 1.36 106 87 151 64 304.67 0.80 107 88 124 36 426.51 9.66 108 88 128 40 359.29 3.00 109 88 131 43 359.19 2.96 110 88 132 44 358.48 3.30 111 88 151 63 295.86 1.39 112 89 121 32 451.50 0.24 113 89 124 35 381.67 2.44 114 89 151 62 296.09 1.28 115 90 121 31 451.46 0.21 116 90 125 35 359.58 2.85 117 94 125 31 359.17 2.98 118 95 125 30 359.11 3.00 119 95 128 33 357.20 3.21 120 95 129 34 334.80 2.54 121 95 132 37 324.05 4.11 122 98 125 27 358.45 3.26 123 98 126 28 358.33 3.23 124 98 129 31 324.11 4.05 125 99 129 30 324.11 4.06 126 99 132 33 322.70 4.38 127 99 133 34 310.95 0.17 128 102 114 12 525.97 4.17 129 102 116 14 451.79 0.27 130 102 129 27 324.11 4.05 131 102 130 28 324.01 4.08 132 102 133 31 309.97 0.66 133 102 137 35 309.75 0.69 134 102 141 39 309.58 0.72 135 103 137 34 309.73 0.68 136 105 114 9 482.50 14.09 137 106 137 31 309.69 0.67 138 106 140 34 309.61 0.71 139 109 112 3 451.56 0.18 140 110 140 30 309.56 0.72 141 111 211 100 40.52 0.78 142 113 142 29 309.29 0.77 143 113 207 94 80.05 0.66 144 113 210 97 40.59 0.83 145 113 211 98 37.68 0.63 146 114 137 23 309.75 0.69 147 114 140 26 309.58 0.71 148 114 141 27 309.50 0.70 149 114 142 28 309.45 0.71 150 115 141 26 309.53 0.71 151 115 142 27 309.50 0.70 152 115 143 28 309.23 0.74 153 115 203 88 102.80 0.77 154 115 207 92 80.20 0.60 155 116 141 25 309.60 0.72 156 116 143 27 309.46 0.71 157 116 144 28 309.03 0.68 158 116 145 29 308.19 0.28 159 116 203 87 105.68 0.08 160 117 144 27 309.34 0.75 161 117 145 28 308.31 0.34 162 118 122 4 359.50 2.78 163 118 123 5 358.94 3.00 164 118 145 27 309.30 0.77 165 118 146 28 308.30 0.34 166 118 147 29 307.23 0.47 167 119 122 3 366.11 2.77 168 119 123 4 359.61 2.84 169 119 147 28 307.23 0.48 170 119 188 69 118.00 1.84 171 119 189 70 117.94 1.85 172 119 191 72 115.84 1.33 173 120 123 3 370.21 1.13 174 120 124 4 365.53 0.02 175 120 147 27 309.27 0.76 176 120 148 28 306.86 0.65 177 120 150 30 298.97 0.45 178 120 188 68 117.99 1.82 179 121 124 3 369.80 0.92 180 121 125 4 365.41 0.05 181 121 150 29 295.97 1.22 182 122 125 3 369.41 2.05 183 122 126 4 365.42 0.07 184 123 126 3 369.39 2.06 185 123 127 4 365.63 0.01 186 123 146 23 309.27 0.76 187 123 147 24 309.25 0.75 188 123 149 26 293.13 0.02 189 124 127 3 365.64 0.01 190 124 128 4 365.64 0.00 191 124 149 25 298.42 0.80 192 124 150 26 292.03 0.53 193 124 151 27 291.54 0.35 194 125 128 3 369.58 1.97 195 125 129 4 365.55 0.04 196 126 129 3 365.61 0.01 197 126 130 4 365.54 0.04 198 126 146 20 309.31 0.73 199 127 130 3 367.42 0.89 200 127 131 4 357.31 4.05 201 127 149 22 299.89 0.06 202 127 159 32 220.19 0.09 203 128 131 3 368.35 1.27 204 128 132 4 356.63 3.71 205 129 132 3 365.81 5.33 206 129 133 4 357.12 3.97 207 130 133 3 359.28 2.89 208 130 138 8 309.90 0.62 209 130 141 11 309.82 0.67 210 130 144 14 309.58 0.73 211 130 159 29 220.19 0.09 212 130 162 32 219.82 0.15 213 131 138 7 311.00 0.28 214 131 160 29 220.10 0.10 215 131 161 30 220.08 0.10 216 133 137 4 351.10 4.97 217 133 138 5 311.28 0.39 218 133 141 8 310.99 0.28 219 134 137 3 382.97 0.53 220 134 138 4 348.18 7.76 221 135 138 3 378.61 2.71 222 135 139 4 347.09 5.62 223 136 140 4 356.56 4.62 224 137 140 3 368.27 1.24 225 137 141 4 368.26 1.24 226 138 141 3 381.83 4.17 227 138 161 23 219.81 0.14 228 138 162 24 219.59 0.12 229 139 166 27 218.99 0.04 230 141 144 3 411.41 0.80 231 141 162 21 219.53 0.20 232 141 166 25 218.88 0.04 233 142 166 24 218.83 0.04 234 142 206 64 84.25 0.59 235 142 207 65 83.52 0.94 236 142 210 68 77.11 0.72 237 143 162 19 219.72 0.12 238 143 166 23 218.84 0.04 239 143 202 59 108.78 0.57 240 143 203 60 106.25 0.06 241 143 206 63 84.28 0.60 242 144 159 15 220.23 0.07 243 144 162 18 219.69 0.14 244 144 166 22 218.95 0.06 245 144 167 23 218.82 0.04 246 144 168 24 218.80 0.03 247 144 202 58 109.42 0.58 248 144 203 59 107.91 0.62 249 145 168 23 218.79 0.03 250 145 170 25 218.75 0.04 251 145 199 54 109.69 0.50 252 145 202 57 109.52 0.53 253 145 203 58 108.64 0.55 254 146 149 3 373.54 1.36 255 146 159 13 220.25 0.06 256 146 167 21 219.00 0.09 257 146 168 22 218.88 0.04 258 146 169 23 218.77 0.03 259 146 170 24 218.74 0.04 260 147 170 23 218.50 0.04 261 147 191 44 115.84 1.33 262 147 194 47 115.54 1.43 263 147 195 48 115.73 1.36 264 147 199 52 115.25 1.33 265 148 170 22 218.80 0.03 266 148 171 23 218.68 0.06 267 148 175 27 218.61 0.10 268 148 177 29 217.75 0.31 269 148 178 30 217.08 0.51 270 148 188 40 118.00 1.84 271 148 191 43 115.95 1.38 272 149 152 3 370.78 0.74 273 149 155 6 318.69 0.24 274 149 158 9 220.72 0.14 275 149 159 10 220.38 0.04 276 149 169 20 218.88 0.04 277 149 171 22 218.77 0.03 278 149 177 28 217.75 0.31 279 149 178 29 216.34 0.77 280 150 154 4 383.62 2.02 281 150 177 27 217.41 0.48 282 151 154 3 373.15 1.52 283 151 155 4 349.28 5.14 284 152 155 3 373.38 1.32 285 152 156 4 326.11 3.47 286 152 157 5 220.93 0.12 287 152 169 17 219.11 0.08 288 152 171 19 218.90 0.04 289 152 178 26 216.69 0.71 290 153 156 3 350.36 5.67 291 153 178 25 218.27 0.23 292 153 179 26 216.46 0.83 293 153 180 27 215.91 0.98 294 154 180 26 215.67 0.46 295 155 158 3 368.73 0.73 296 155 160 5 238.03 8.69 297 157 169 12 219.17 0.06 298 158 162 4 364.82 4.30 299 158 163 5 248.19 4.17 300 158 164 6 220.27 0.32 301 159 162 3 370.02 1.24 302 159 167 8 219.80 0.35 303 162 166 4 371.65 2.13 304 162 167 5 337.51 12.01 305 163 166 3 377.81 0.95 306 163 167 4 364.47 1.46 307 164 167 3 364.47 1.46 308 165 202 37 109.68 0.48 309 165 206 41 106.04 0.10 310 166 202 36 109.66 0.48 311 167 202 35 109.68 0.48 312 168 202 34 109.68 0.48 313 170 191 21 115.95 1.39 314 170 194 24 115.53 1.43 315 170 198 28 115.41 1.40 316 170 199 29 115.28 1.33 317 171 191 20 117.91 1.85 318 172 187 15 120.25 1.20 319 172 190 18 119.23 1.27 320 172 191 19 118.83 1.45 321 173 187 14 128.47 2.16 322 174 185 11 140.84 0.24 323 174 187 13 129.52 1.63 324 175 187 12 128.47 2.16 325 175 188 13 122.96 0.04 326 175 191 16 123.51 0.32 327 176 181 5 440.46 3.00 328 176 183 7 344.93 6.98 329 176 185 9 137.55 1.87 330 177 181 4 400.08 1.46 331 177 182 5 373.52 1.99 332 177 183 6 344.94 6.98 333 177 188 11 123.51 0.32 334 184 188 4 349.17 6.15 335 184 189 5 349.31 6.21 336 185 188 3 379.45 1.14 337 186 189 3 387.87 0.58 338 186 190 4 380.07 4.48 339 187 190 3 388.25 0.39 340 187 191 4 388.25 0.39 341 188 191 3 411.06 3.65 342 190 193 3 431.90 0.59 343 191 194 3 370.65 5.42 344 191 195 4 344.76 7.52 345 192 195 3 364.79 2.49 346 192 196 4 364.11 2.16 347 193 196 3 352.48 3.67 348 193 197 4 364.10 2.17 349 193 198 5 344.25 7.28 350 194 197 3 381.93 4.08 351 194 198 4 343.31 7.75 352 194 199 5 342.29 7.57 353 194 200 6 342.99 7.91 354 195 199 4 342.29 7.57 355 195 200 5 342.29 7.57 356 196 200 4 346.66 6.08 357 197 200 3 377.50 1.85 358 197 201 4 345.11 6.42 359 198 201 3 351.79 9.13 360 198 202 4 345.11 6.42 361 199 202 3 363.69 1.92 362 199 203 4 347.18 5.38 363 200 203 3 352.75 2.89 364 200 204 4 347.84 5.73 365 201 204 3 373.57 2.46 366 201 205 4 347.86 5.73 367 202 205 3 366.19 2.72 368 202 206 4 348.61 6.11 369 203 206 3 367.36 2.14 370 203 207 4 348.00 6.41 371 204 207 3 358.18 5.00 372 204 208 4 349.16 6.96 373 205 208 3 349.16 6.96 374 205 209 4 348.00 6.40 375 206 209 3 373.57 2.80 376 206 210 4 373.23 2.62 377 207 210 3 380.31 3.51 378 207 211 4 345.61 6.71 379 208 211 3 364.73 6.87 380 208 212 4 279.85 21.74