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 27 127.27 7.50 2 18 46 28 138.82 1.73 3 18 47 29 127.28 7.50 4 18 48 30 127.23 7.50 5 18 49 31 127.23 7.50 6 18 53 35 128.28 7.07 7 19 46 27 141.83 3.23 8 19 47 28 141.65 3.14 9 20 47 27 145.88 2.52 10 20 48 28 145.25 2.25 11 20 60 40 169.60 1.61 12 20 65 45 169.75 1.65 13 20 70 50 153.81 2.00 14 20 71 51 145.25 2.25 15 20 72 52 145.25 2.25 16 21 24 3 368.96 0.58 17 21 25 4 320.85 3.10 18 21 47 26 162.48 0.18 19 21 71 50 151.61 0.34 20 22 25 3 371.97 2.08 21 22 26 4 320.75 3.06 22 22 69 47 169.60 1.60 23 22 70 48 169.31 1.53 24 22 71 49 169.28 1.54 25 23 26 3 367.63 0.09 26 23 35 12 169.63 1.61 27 23 37 14 169.59 1.61 28 23 69 46 169.69 1.63 29 23 71 48 169.44 1.54 30 23 101 78 169.74 1.68 31 23 104 81 170.55 1.28 32 23 105 82 169.74 1.67 33 23 108 85 170.99 1.33 34 24 71 47 169.77 1.67 35 24 101 77 169.75 1.68 36 24 104 80 169.78 1.69 37 24 108 84 171.53 1.14 38 26 69 43 169.81 1.66 39 26 108 82 173.43 0.71 40 27 30 3 372.81 0.23 41 27 31 4 357.42 6.32 42 27 69 42 528.33 4.41 43 28 31 3 372.81 0.23 44 28 108 80 240.68 11.21 45 32 112 80 448.43 0.58 46 33 112 79 448.43 0.58 47 33 113 80 448.42 0.58 48 33 211 178 34.00 1.66 49 34 113 79 448.44 0.58 50 34 115 81 448.41 0.58 51 34 207 173 45.40 1.09 52 34 211 177 34.01 1.67 53 35 112 77 506.72 5.09 54 35 113 78 455.56 2.20 55 35 114 79 448.44 0.58 56 35 115 80 448.43 0.58 57 36 115 79 448.44 0.58 58 36 116 80 448.42 0.58 59 36 117 81 448.42 0.58 60 36 203 167 62.12 0.34 61 37 115 78 449.51 0.68 62 37 116 79 448.43 0.57 63 37 117 80 448.43 0.57 64 38 117 79 448.44 0.58 65 38 118 80 448.43 0.57 66 38 119 81 448.43 0.57 67 39 117 78 448.94 0.45 68 39 118 79 448.43 0.57 69 39 119 80 448.43 0.57 70 39 122 83 364.50 0.14 71 39 125 86 363.99 0.24 72 40 119 79 448.44 0.57 73 40 122 82 364.51 0.14 74 41 119 78 448.49 0.58 75 41 120 79 448.44 0.57 76 42 121 79 448.44 0.57 77 44 119 75 449.55 0.74 78 51 119 68 448.19 0.48 79 51 147 96 305.12 0.24 80 51 191 140 70.67 0.37 81 51 192 141 70.13 0.35 82 51 195 144 68.10 0.06 83 54 195 141 68.13 0.07 84 54 196 142 68.13 0.07 85 55 147 92 305.11 0.24 86 55 195 140 68.14 0.07 87 55 200 145 65.58 0.66 88 55 203 148 62.37 0.47 89 58 196 138 69.48 0.58 90 58 200 142 66.61 0.73 91 59 115 56 448.46 0.57 92 59 200 141 65.59 0.67 93 59 203 144 62.44 0.51 94 59 204 145 62.02 0.39 95 62 204 142 62.04 0.40 96 63 204 141 62.02 0.41 97 63 207 144 52.47 2.19 98 73 125 52 363.99 0.23 99 77 121 44 448.66 0.46 100 77 122 45 447.86 0.49 101 77 125 48 364.26 0.22 102 79 121 42 448.68 0.47 103 80 121 41 448.88 0.45 104 83 121 38 448.82 0.46 105 84 121 37 448.77 0.45 106 84 182 98 181.46 1.54 107 85 182 97 183.90 2.75 108 87 151 64 307.57 0.32 109 88 128 40 364.24 0.18 110 88 131 43 364.13 0.14 111 88 132 44 363.87 0.24 112 88 151 63 297.63 2.42 113 89 121 32 448.67 0.46 114 89 124 35 384.81 4.52 115 89 151 62 297.63 2.42 116 90 121 31 448.43 0.57 117 90 125 35 364.56 0.10 118 94 125 31 364.14 0.15 119 95 125 30 364.02 0.24 120 95 128 33 358.06 0.21 121 95 129 34 335.86 0.80 122 98 125 27 363.97 0.24 123 98 126 28 363.57 0.29 124 98 129 31 334.51 0.15 125 99 129 30 334.51 0.15 126 99 132 33 326.06 4.33 127 99 133 34 309.78 0.01 128 102 114 12 517.93 10.88 129 102 116 14 448.68 0.47 130 102 129 27 333.08 0.87 131 102 130 28 330.92 1.94 132 102 133 31 309.56 0.12 133 102 137 35 309.27 0.17 134 102 141 39 308.89 0.22 135 103 133 30 309.57 0.12 136 103 137 34 309.27 0.17 137 105 114 9 450.49 0.23 138 106 137 31 309.22 0.15 139 106 140 34 308.89 0.22 140 109 112 3 448.43 0.58 141 110 140 30 308.81 0.23 142 111 211 100 34.99 1.28 143 113 142 29 308.63 0.15 144 113 207 94 46.05 0.96 145 113 210 97 37.32 0.42 146 113 211 98 33.98 1.66 147 114 137 23 309.28 0.18 148 114 140 26 308.87 0.23 149 114 141 27 308.75 0.20 150 114 142 28 308.74 0.19 151 115 141 26 308.85 0.23 152 115 142 27 308.79 0.21 153 115 143 28 308.59 0.18 154 115 203 88 62.12 0.34 155 115 207 92 45.66 0.95 156 116 141 25 308.89 0.22 157 116 143 27 308.78 0.21 158 116 144 28 308.06 0.32 159 116 145 29 307.82 0.44 160 117 144 27 308.73 0.19 161 117 145 28 308.06 0.33 162 118 122 4 364.52 0.14 163 118 123 5 364.20 0.26 164 118 145 27 308.74 0.19 165 118 146 28 306.11 0.24 166 118 147 29 306.08 0.24 167 119 122 3 366.96 1.04 168 119 123 4 364.59 0.10 169 119 147 28 306.07 0.23 170 119 188 69 71.76 0.45 171 119 189 70 71.69 0.42 172 119 191 72 70.69 0.38 173 120 123 3 367.00 1.02 174 120 124 4 367.00 1.02 175 120 147 27 308.65 0.15 176 120 148 28 306.07 0.24 177 120 150 30 297.74 2.37 178 120 188 68 71.74 0.45 179 121 124 3 370.12 0.55 180 121 125 4 369.00 2.01 181 121 150 29 297.58 2.46 182 122 125 3 369.00 2.01 183 122 126 4 368.75 2.13 184 123 126 3 371.57 0.72 185 123 127 4 368.75 2.13 186 123 146 23 308.72 0.19 187 123 147 24 308.59 0.18 188 123 149 26 297.63 2.43 189 124 127 3 370.07 1.48 190 124 128 4 368.75 2.14 191 124 149 25 298.00 2.56 192 124 150 26 297.54 2.44 193 124 151 27 290.80 0.58 194 125 128 3 369.14 1.93 195 125 129 4 352.68 0.95 196 126 129 3 381.14 0.18 197 126 130 4 359.73 2.64 198 126 146 20 308.73 0.18 199 127 130 3 381.13 0.18 200 127 131 4 355.26 0.41 201 127 149 22 298.04 2.58 202 127 159 32 221.16 1.79 203 128 131 3 366.35 0.86 204 128 132 4 359.73 2.64 205 129 132 3 360.36 2.13 206 129 133 4 354.87 0.60 207 130 133 3 360.62 4.32 208 130 138 8 309.30 0.16 209 130 141 11 309.31 0.15 210 130 144 14 308.90 0.22 211 130 159 29 221.16 1.79 212 130 162 32 220.71 1.64 213 131 138 7 309.63 0.16 214 131 160 29 221.15 1.80 215 131 161 30 221.06 1.79 216 133 137 4 373.97 2.83 217 133 138 5 328.38 0.40 218 133 141 8 309.70 0.17 219 134 137 3 379.50 0.09 220 134 138 4 349.54 9.38 221 135 138 3 374.41 2.62 222 135 139 4 349.54 9.38 223 136 140 4 369.80 1.62 224 137 140 3 384.38 0.92 225 138 141 3 380.80 2.74 226 138 161 23 220.99 1.75 227 138 162 24 220.60 1.69 228 139 166 27 220.21 1.73 229 141 144 3 426.33 0.14 230 141 162 21 220.72 1.62 231 141 166 25 220.16 1.75 232 142 166 24 220.16 1.75 233 142 206 64 55.48 1.09 234 142 210 68 42.41 0.51 235 143 162 19 220.76 1.64 236 143 166 23 220.16 1.75 237 143 203 60 62.63 0.49 238 143 206 63 51.72 0.79 239 144 159 15 221.28 1.75 240 144 162 18 220.75 1.64 241 144 166 22 220.21 1.73 242 144 167 23 220.01 1.71 243 144 168 24 220.01 1.71 244 145 168 23 220.01 1.71 245 145 170 25 219.87 1.65 246 145 199 54 67.11 0.59 247 145 202 57 66.53 0.71 248 145 203 58 62.91 0.62 249 146 149 3 378.92 2.46 250 146 159 13 221.28 1.75 251 146 167 21 220.33 1.67 252 146 168 22 220.17 1.69 253 146 169 23 219.93 1.72 254 146 170 24 219.84 1.68 255 147 170 23 219.66 1.64 256 147 191 44 71.06 0.55 257 147 194 47 70.64 0.38 258 147 195 48 70.63 0.39 259 147 199 52 70.20 0.48 260 148 170 22 220.00 1.72 261 148 171 23 219.69 1.62 262 148 175 27 219.66 1.64 263 148 177 29 219.66 1.64 264 148 178 30 219.53 1.65 265 148 188 40 71.77 0.45 266 148 191 43 71.28 0.43 267 149 152 3 366.88 0.21 268 149 155 6 321.90 4.91 269 149 158 9 221.39 1.74 270 149 169 20 220.16 1.71 271 149 171 22 219.86 1.69 272 149 177 28 219.66 1.64 273 149 178 29 219.47 1.62 274 150 154 4 379.39 0.49 275 150 177 27 219.62 1.62 276 151 154 3 369.21 0.76 277 151 155 4 350.68 9.48 278 152 155 3 371.63 1.65 279 152 156 4 322.15 4.42 280 152 157 5 269.20 22.03 281 152 169 17 220.37 1.66 282 152 171 19 220.03 1.71 283 152 178 26 219.57 1.64 284 153 156 3 367.50 1.09 285 153 178 25 219.77 1.70 286 153 179 26 219.50 1.60 287 153 180 27 216.53 0.16 288 154 180 26 216.23 0.33 289 155 158 3 365.20 0.08 290 155 160 5 221.90 1.81 291 157 169 12 220.33 1.68 292 158 162 4 351.75 7.52 293 158 163 5 269.96 20.23 294 158 164 6 221.16 1.41 295 159 162 3 357.36 4.71 296 159 167 8 220.96 1.36 297 162 166 4 360.33 2.86 298 162 167 5 331.38 0.28 299 163 166 3 369.12 0.94 300 163 167 4 340.86 0.71 301 164 167 3 359.00 9.79 302 165 206 41 63.52 0.32 303 166 202 36 66.75 0.79 304 167 202 35 66.82 0.76 305 168 202 34 66.76 0.79 306 170 191 21 72.09 0.21 307 170 194 24 70.84 0.46 308 170 198 28 70.66 0.38 309 170 199 29 70.62 0.38 310 171 191 20 72.32 0.27 311 172 187 15 73.31 0.32 312 172 190 18 73.18 0.12 313 172 191 19 72.44 0.25 314 172 194 22 72.19 0.23 315 173 187 14 74.17 0.59 316 174 185 11 74.83 0.79 317 174 187 13 74.17 0.59 318 175 187 12 74.14 0.58 319 175 188 13 74.14 0.58 320 175 191 16 74.14 0.58 321 176 181 5 479.89 0.21 322 176 183 7 321.88 4.71 323 177 181 4 405.68 1.65 324 177 182 5 371.51 0.57 325 177 183 6 321.88 4.69 326 177 188 11 74.13 0.58 327 184 188 4 354.23 5.94 328 184 189 5 370.46 1.79 329 185 188 3 379.63 2.80 330 186 189 3 387.38 0.49 331 186 190 4 371.38 1.32 332 187 190 3 390.69 1.16 333 187 191 4 390.69 1.16 334 188 191 3 409.73 1.74 335 190 193 3 428.61 2.58 336 191 194 3 387.38 2.91 337 191 195 4 356.39 7.67 338 192 195 3 370.91 0.41 339 192 196 4 356.38 7.67 340 193 196 3 363.32 4.20 341 193 197 4 353.70 6.33 342 193 198 5 353.66 6.34 343 194 197 3 381.62 0.70 344 194 198 4 336.06 2.44 345 194 199 5 335.84 2.33 346 194 200 6 335.85 2.33 347 195 199 4 335.10 2.71 348 195 200 5 335.10 2.71 349 196 200 4 354.29 5.20 350 197 200 3 376.61 0.72 351 197 201 4 336.77 3.56 352 198 201 3 346.85 1.39 353 198 202 4 355.25 5.69 354 199 202 3 358.88 6.84 355 199 203 4 355.25 5.69 356 200 203 3 358.82 6.82 357 200 204 4 337.06 3.41 358 201 204 3 354.82 5.90 359 201 205 4 352.42 7.09 360 202 205 3 354.81 5.90 361 202 206 4 352.42 7.09 362 203 206 3 356.51 5.05 363 203 207 4 353.28 6.67 364 204 207 3 361.22 2.69 365 204 208 4 355.12 5.74 366 205 208 3 355.12 5.74 367 205 209 4 353.26 6.66 368 206 209 3 367.78 0.60 369 206 210 4 367.79 0.61 370 207 210 3 380.28 1.12 371 207 211 4 355.11 5.73 372 208 211 3 367.75 0.62 373 208 212 4 155.73 33.85