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 46 28 63.29 0.21 2 18 47 29 63.18 0.20 3 18 48 30 56.95 0.26 4 18 49 31 61.12 0.35 5 18 53 35 47.29 1.47 6 19 46 27 63.40 0.18 7 19 47 28 63.37 0.16 8 19 48 29 63.18 0.20 9 20 47 27 63.83 0.27 10 20 48 28 63.42 0.18 11 20 60 40 63.30 0.12 12 20 65 45 63.37 0.29 13 20 70 50 63.22 0.23 14 20 71 51 63.40 0.18 15 20 72 52 63.53 0.12 16 21 24 3 385.62 3.83 17 21 25 4 334.79 12.98 18 21 71 50 63.73 0.23 19 22 26 4 276.77 30.11 20 22 69 47 64.25 0.04 21 22 70 48 64.47 0.14 22 22 71 49 64.59 0.12 23 23 26 3 333.07 1.96 24 23 35 12 64.61 0.12 25 23 37 14 65.47 0.10 26 23 69 46 64.61 0.12 27 23 71 48 65.24 0.20 28 23 101 78 66.18 0.24 29 23 104 81 66.18 0.24 30 23 105 82 65.95 0.15 31 23 108 85 66.04 0.19 32 24 71 47 65.99 0.13 33 24 101 77 66.25 0.21 34 24 104 80 66.28 0.21 35 24 108 84 126.78 0.57 36 25 108 83 219.44 0.43 37 26 69 43 66.09 0.13 38 26 108 82 175.08 22.62 39 27 30 3 350.91 4.83 40 27 31 4 348.87 5.85 41 27 69 42 535.32 3.12 42 28 31 3 355.18 4.90 43 28 108 80 203.84 8.25 44 32 112 80 458.53 0.05 45 33 112 79 458.53 0.05 46 33 113 80 458.53 0.05 47 33 211 178 37.48 0.16 48 34 113 79 458.53 0.05 49 34 115 81 458.52 0.05 50 34 207 173 82.28 0.46 51 35 112 77 493.30 16.05 52 35 113 78 462.10 0.52 53 35 114 79 458.54 0.05 54 35 115 80 458.53 0.05 55 36 115 79 458.54 0.05 56 36 116 80 458.53 0.04 57 36 117 81 458.53 0.05 58 36 203 167 97.88 1.32 59 37 115 78 461.99 0.58 60 37 116 79 458.55 0.05 61 37 117 80 458.54 0.05 62 38 117 79 458.55 0.05 63 38 118 80 458.54 0.04 64 38 119 81 458.54 0.05 65 39 117 78 460.85 0.52 66 39 118 79 458.55 0.05 67 39 119 80 458.55 0.05 68 39 122 83 361.00 1.80 69 39 125 86 360.89 1.76 70 40 119 79 458.56 0.06 71 40 122 82 361.01 1.80 72 41 119 78 458.69 0.04 73 41 120 79 458.56 0.06 74 41 121 80 458.50 0.06 75 42 121 79 458.57 0.06 76 44 119 75 461.82 0.70 77 51 119 68 458.60 0.06 78 51 147 96 299.93 0.10 79 51 191 140 109.44 0.51 80 51 192 141 109.00 0.46 81 51 195 144 105.30 0.31 82 54 195 141 105.32 0.33 83 54 196 142 105.31 0.33 84 55 147 92 300.38 0.10 85 55 195 140 105.30 0.31 86 55 199 144 104.99 0.28 87 55 200 145 104.38 0.01 88 55 203 148 103.76 0.04 89 58 196 138 105.31 0.33 90 58 200 142 104.37 0.01 91 58 204 146 97.86 1.33 92 59 115 56 461.20 0.16 93 59 203 144 97.87 1.33 94 59 204 145 97.30 1.16 95 62 204 142 97.28 1.17 96 62 208 146 87.08 0.26 97 63 204 141 97.25 1.18 98 63 207 144 87.06 0.30 99 63 208 145 84.50 1.50 100 73 125 52 360.91 1.75 101 77 121 44 458.53 0.04 102 77 122 45 441.91 7.71 103 77 125 48 360.96 1.77 104 79 121 42 458.58 0.06 105 80 121 41 459.10 0.14 106 83 121 38 460.81 0.53 107 84 121 37 460.52 0.70 108 84 182 98 178.68 1.98 109 85 182 97 185.14 0.83 110 88 124 36 435.31 4.48 111 88 128 40 361.99 1.35 112 88 131 43 360.95 1.73 113 88 132 44 360.94 1.73 114 88 151 63 293.13 1.04 115 89 121 32 458.60 0.07 116 89 124 35 399.69 0.61 117 89 151 62 293.13 1.04 118 90 121 31 458.58 0.07 119 90 125 35 364.41 0.85 120 94 125 31 360.95 1.77 121 95 125 30 360.95 1.77 122 95 128 33 357.31 2.43 123 95 129 34 323.55 4.36 124 95 132 37 322.81 4.05 125 98 116 18 462.33 0.75 126 98 125 27 360.89 1.75 127 98 126 28 360.51 1.73 128 98 129 31 322.88 4.08 129 99 129 30 322.87 4.08 130 99 132 33 321.75 3.75 131 99 133 34 307.22 0.69 132 102 116 14 461.22 1.20 133 102 129 27 322.87 4.08 134 102 130 28 322.80 4.09 135 102 133 31 304.10 0.27 136 102 137 35 303.56 0.38 137 102 141 39 303.16 0.48 138 103 137 34 303.55 0.37 139 105 114 9 492.30 14.34 140 106 137 31 303.53 0.37 141 106 140 34 303.17 0.48 142 109 112 3 458.54 0.06 143 110 140 30 303.14 0.48 144 111 211 100 39.01 0.04 145 112 211 99 37.61 0.10 146 113 140 27 303.16 0.48 147 113 142 29 303.05 0.48 148 113 207 94 82.31 0.45 149 113 210 97 68.81 0.46 150 113 211 98 37.58 0.09 151 114 137 23 303.54 0.37 152 114 140 26 303.16 0.48 153 114 141 27 303.13 0.48 154 114 142 28 303.04 0.53 155 115 141 26 303.15 0.48 156 115 142 27 303.12 0.49 157 115 143 28 302.64 0.59 158 115 203 88 97.84 1.32 159 115 207 92 86.99 0.23 160 116 141 25 303.17 0.49 161 116 143 27 303.09 0.51 162 116 144 28 302.06 0.73 163 116 145 29 302.03 0.71 164 117 144 27 302.72 0.62 165 117 145 28 302.00 0.72 166 118 122 4 363.99 1.06 167 118 123 5 360.99 1.80 168 118 145 27 302.66 0.61 169 118 146 28 301.44 0.42 170 118 147 29 300.37 0.11 171 119 122 3 369.42 1.61 172 119 123 4 361.76 2.18 173 119 147 28 299.93 0.10 174 119 188 69 111.27 0.60 175 119 189 70 111.26 0.60 176 119 191 72 109.49 0.52 177 120 123 3 379.36 1.62 178 120 124 4 375.69 0.67 179 120 147 27 302.15 0.70 180 120 148 28 300.37 0.10 181 120 150 30 295.82 0.30 182 120 188 68 111.27 0.60 183 121 124 3 375.69 0.67 184 121 125 4 365.14 0.52 185 122 125 3 370.87 3.08 186 122 126 4 364.40 0.15 187 123 126 3 364.44 0.14 188 123 127 4 364.45 0.12 189 123 146 23 302.28 0.76 190 123 149 26 294.25 0.48 191 124 127 3 364.49 0.14 192 124 128 4 364.31 0.06 193 124 149 25 296.76 0.16 194 124 150 26 293.13 1.04 195 124 151 27 288.48 0.97 196 125 128 3 365.22 0.51 197 125 129 4 354.95 4.62 198 126 129 3 370.10 0.80 199 126 130 4 352.56 1.71 200 126 146 20 302.48 0.70 201 127 130 3 376.83 0.53 202 127 131 4 352.51 1.74 203 127 149 22 295.20 0.03 204 127 155 28 218.39 0.85 205 127 159 32 216.69 0.46 206 127 160 33 216.69 0.46 207 128 131 3 366.10 1.30 208 128 132 4 352.58 1.70 209 129 132 3 362.67 2.27 210 129 133 4 347.71 4.13 211 130 133 3 359.43 1.72 212 130 138 8 303.98 0.21 213 130 141 11 303.60 0.41 214 130 144 14 303.16 0.51 215 130 159 29 216.69 0.46 216 130 162 32 216.22 0.63 217 131 138 7 311.43 2.65 218 131 160 29 216.65 0.45 219 131 161 30 216.62 0.44 220 133 137 4 364.88 0.08 221 133 138 5 323.97 3.37 222 133 141 8 307.08 0.59 223 134 137 3 374.25 2.89 224 134 138 4 364.88 0.09 225 135 138 3 364.89 0.09 226 135 139 4 364.89 0.09 227 136 139 3 379.89 1.01 228 136 140 4 379.08 1.41 229 137 140 3 379.08 1.42 230 138 141 3 373.41 1.43 231 138 161 23 216.30 0.61 232 138 162 24 216.11 0.68 233 139 166 27 215.32 0.41 234 141 144 3 437.19 2.27 235 141 162 21 216.13 0.67 236 141 166 25 215.30 0.42 237 142 166 24 215.31 0.41 238 142 206 64 89.20 0.73 239 142 207 65 87.06 0.29 240 142 210 68 70.61 0.45 241 143 162 19 216.34 0.63 242 143 166 23 215.30 0.42 243 143 203 60 101.05 1.43 244 143 206 63 92.17 0.75 245 144 159 15 216.72 0.48 246 144 162 18 216.34 0.63 247 144 166 22 215.33 0.41 248 144 167 23 215.19 0.39 249 144 168 24 215.16 0.40 250 144 202 58 105.06 0.24 251 144 203 59 103.14 0.64 252 145 168 23 215.14 0.40 253 145 170 25 214.72 0.45 254 145 199 54 105.00 0.29 255 145 202 57 105.11 0.26 256 145 203 58 104.67 0.17 257 146 149 3 383.98 1.03 258 146 159 13 216.75 0.49 259 146 168 22 215.18 0.39 260 146 169 23 214.87 0.38 261 146 170 24 214.71 0.45 262 147 170 23 214.32 0.27 263 147 191 44 109.50 0.52 264 147 194 47 109.43 0.51 265 147 195 48 109.28 0.47 266 147 199 52 108.85 0.40 267 148 170 22 215.00 0.39 268 148 171 23 214.13 0.36 269 148 177 29 212.40 0.03 270 148 178 30 211.45 0.35 271 148 188 40 111.27 0.60 272 148 191 43 109.51 0.51 273 149 152 3 370.79 2.85 274 149 155 6 315.91 0.10 275 149 158 9 216.94 0.45 276 149 169 20 215.21 0.38 277 149 171 22 214.88 0.36 278 149 178 29 211.44 0.35 279 150 154 4 383.93 0.77 280 150 177 27 211.72 0.21 281 151 154 3 378.78 1.80 282 151 155 4 348.46 7.28 283 152 155 3 382.85 0.23 284 152 156 4 339.62 11.71 285 152 157 5 219.88 0.97 286 152 169 17 215.43 0.41 287 152 171 19 215.25 0.39 288 152 178 26 211.77 0.19 289 153 156 3 352.30 5.38 290 153 178 25 214.11 0.27 291 153 179 26 211.56 0.29 292 153 180 27 208.05 1.99 293 154 180 26 207.06 1.49 294 155 158 3 370.37 0.10 295 155 160 5 216.84 0.43 296 157 169 12 215.44 0.42 297 159 162 3 341.60 13.79 298 159 167 8 215.46 0.42 299 162 166 4 376.81 1.45 300 162 167 5 234.52 3.64 301 163 166 3 376.81 1.45 302 163 167 4 366.45 3.73 303 164 167 3 376.86 1.43 304 165 206 41 101.53 1.19 305 166 202 36 105.18 0.29 306 166 206 40 97.84 1.32 307 166 210 44 87.11 0.26 308 167 202 35 105.20 0.29 309 168 202 34 105.22 0.30 310 170 191 21 110.78 0.76 311 170 194 24 109.44 0.50 312 170 198 28 109.14 0.39 313 170 199 29 109.04 0.36 314 171 191 20 111.17 0.61 315 172 187 15 122.52 0.50 316 172 190 18 116.87 1.44 317 172 191 19 111.27 0.61 318 173 187 14 137.91 2.00 319 174 185 11 188.37 14.25 320 174 187 13 137.92 1.99 321 175 187 12 137.18 2.37 322 175 188 13 137.16 2.35 323 175 191 16 129.16 1.45 324 176 181 5 526.70 7.29 325 176 183 7 352.18 4.42 326 176 185 9 195.78 17.96 327 177 181 4 400.97 0.21 328 177 182 5 376.49 2.60 329 177 183 6 340.09 10.45 330 177 184 7 201.18 15.31 331 177 188 11 131.96 0.04 332 184 188 4 349.92 5.49 333 184 189 5 365.44 2.14 334 185 188 3 382.14 1.49 335 186 189 3 388.35 0.83 336 187 190 3 380.55 3.08 337 187 191 4 388.36 0.83 338 188 191 3 426.26 1.24 339 191 194 3 373.98 1.34 340 191 195 4 330.30 0.18 341 192 195 3 369.15 1.19 342 192 196 4 330.05 0.04 343 193 196 3 368.31 0.29 344 193 197 4 338.97 10.12 345 193 198 5 323.08 2.18 346 194 197 3 363.47 2.14 347 194 198 4 323.07 2.18 348 194 199 5 323.05 2.18 349 195 199 4 323.06 2.18 350 195 200 5 323.06 2.18 351 196 200 4 354.67 6.58 352 197 200 3 388.40 3.40 353 197 201 4 336.98 0.83 354 198 201 3 367.45 0.47 355 198 202 4 351.48 6.42 356 199 202 3 372.04 2.20 357 199 203 4 366.42 0.04 358 200 203 3 367.44 0.47 359 200 204 4 366.41 0.04 360 201 204 3 367.43 0.47 361 201 205 4 366.41 0.04 362 202 205 3 366.42 0.04 363 202 206 4 366.42 0.04 364 203 206 3 364.82 0.81 365 203 207 4 366.49 2.04 366 204 207 3 371.94 0.68 367 204 208 4 357.85 6.37 368 205 208 3 372.90 1.16 369 205 209 4 357.85 6.37 370 206 209 3 373.58 0.82 371 206 210 4 371.94 0.68 372 207 210 3 373.65 0.84 373 207 211 4 344.17 0.46 374 208 211 3 370.30 0.82 375 208 212 4 318.74 0.12 376 208 213 5 177.62 24.19