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 59.58 1.03 2 18 46 28 59.58 1.03 3 18 47 29 59.56 1.03 4 18 48 30 53.24 1.67 5 18 49 31 57.15 0.30 6 18 53 35 44.16 0.97 7 19 46 27 59.94 0.86 8 19 47 28 59.61 1.02 9 20 47 27 60.31 1.02 10 20 48 28 60.23 0.98 11 20 60 40 59.87 0.87 12 20 70 50 59.87 0.87 13 20 71 51 60.16 1.02 14 20 72 52 60.25 0.98 15 21 24 3 342.44 0.46 16 21 25 4 183.24 17.18 17 21 71 50 61.79 0.32 18 22 26 4 200.05 27.52 19 22 69 47 62.09 0.43 20 22 70 48 62.53 0.23 21 22 71 49 62.66 0.21 22 23 26 3 364.06 10.73 23 23 35 12 62.68 0.23 24 23 37 14 63.24 0.35 25 23 69 46 62.68 0.22 26 23 71 48 63.09 0.42 27 23 101 78 65.45 0.78 28 23 104 81 65.49 0.80 29 23 105 82 64.59 0.66 30 23 108 85 65.34 0.87 31 24 71 47 65.09 0.94 32 24 101 77 65.50 0.79 33 24 104 80 65.61 0.82 34 24 108 84 65.72 0.89 35 26 69 43 65.72 0.92 36 26 108 82 174.89 21.12 37 27 30 3 363.59 0.43 38 27 31 4 240.62 41.09 39 27 69 42 541.32 0.32 40 28 31 3 352.55 5.21 41 28 108 80 183.74 16.71 42 33 112 79 454.96 1.92 43 33 113 80 454.95 1.92 44 33 211 178 35.44 0.96 45 34 113 79 454.95 1.92 46 34 115 81 454.95 1.91 47 34 207 173 80.44 0.46 48 35 112 77 516.89 4.79 49 35 113 78 456.31 1.82 50 35 114 79 454.97 1.91 51 35 115 80 454.97 1.91 52 36 115 79 454.97 1.91 53 36 116 80 454.97 1.91 54 36 117 81 454.95 1.91 55 36 203 167 96.25 0.54 56 37 115 78 455.85 1.72 57 37 116 79 454.97 1.91 58 37 117 80 454.97 1.91 59 38 117 79 454.97 1.91 60 38 118 80 454.96 1.91 61 38 119 81 454.97 1.91 62 39 117 78 455.25 1.82 63 39 118 79 454.96 1.91 64 39 119 80 454.97 1.91 65 39 122 83 365.14 0.93 66 39 125 86 361.03 0.07 67 40 119 79 454.98 1.91 68 40 122 82 365.20 0.90 69 41 119 78 455.16 1.83 70 41 120 79 454.97 1.91 71 41 121 80 454.94 1.91 72 41 122 81 405.57 1.93 73 42 121 79 454.98 1.91 74 44 119 75 455.23 1.85 75 51 119 68 454.84 1.85 76 51 147 96 308.75 0.51 77 51 191 140 111.94 0.77 78 51 192 141 107.22 0.34 79 51 195 144 105.73 0.64 80 54 196 142 105.75 0.64 81 55 147 92 308.75 0.50 82 55 195 140 105.75 0.64 83 55 200 145 105.42 0.60 84 55 203 148 104.95 0.53 85 58 196 138 105.78 0.64 86 58 200 142 105.45 0.62 87 59 115 56 455.00 1.92 88 59 200 141 105.30 0.57 89 59 203 144 95.89 0.73 90 59 204 145 95.77 0.76 91 62 204 142 95.78 0.77 92 63 204 141 95.86 0.73 93 63 207 144 85.75 0.30 94 73 125 52 361.00 0.06 95 77 121 44 454.94 1.93 96 77 122 45 442.29 2.44 97 77 125 48 361.06 0.09 98 79 121 42 454.94 1.93 99 80 121 41 455.12 1.87 100 83 121 38 455.23 1.83 101 84 121 37 455.24 1.82 102 84 182 98 152.32 5.23 103 88 124 36 403.24 3.56 104 88 128 40 362.25 0.18 105 88 132 44 360.76 0.20 106 89 121 32 455.19 1.80 107 89 124 35 389.19 1.92 108 89 151 62 295.57 1.59 109 90 121 31 454.97 1.89 110 90 125 35 363.44 0.15 111 94 125 31 361.15 0.03 112 95 125 30 361.04 0.05 113 95 128 33 356.54 1.04 114 95 129 34 333.99 2.14 115 95 132 37 328.01 0.78 116 98 125 27 360.99 0.07 117 98 126 28 360.95 0.07 118 98 129 31 328.13 0.89 119 99 129 30 328.03 0.87 120 99 132 33 327.14 0.72 121 99 133 34 310.45 0.72 122 102 116 14 455.22 1.81 123 102 129 27 328.03 0.87 124 102 130 28 327.89 0.92 125 102 133 31 310.06 0.53 126 102 137 35 309.92 0.57 127 102 141 39 309.85 0.56 128 105 114 9 455.62 1.63 129 106 137 31 309.85 0.56 130 106 140 34 309.83 0.56 131 109 112 3 454.95 1.92 132 110 140 30 309.81 0.56 133 111 211 100 38.02 0.00 134 113 140 27 309.81 0.57 135 113 142 29 309.62 0.55 136 113 207 94 80.47 0.45 137 113 210 97 38.27 0.12 138 113 211 98 37.98 0.13 139 114 137 23 309.94 0.56 140 114 140 26 309.83 0.56 141 114 141 27 309.79 0.57 142 114 142 28 309.76 0.56 143 115 142 27 309.78 0.58 144 115 143 28 309.58 0.53 145 115 203 88 96.25 0.54 146 115 207 92 85.86 0.62 147 116 130 14 327.57 0.94 148 116 141 25 309.87 0.55 149 116 143 27 309.79 0.58 150 116 144 28 309.45 0.59 151 116 145 29 309.25 0.70 152 117 145 28 309.49 0.58 153 118 122 4 365.14 0.93 154 118 123 5 363.45 0.15 155 118 145 27 309.69 0.58 156 118 146 28 309.39 0.52 157 118 147 29 308.80 0.51 158 119 122 3 384.98 2.35 159 119 123 4 365.16 0.92 160 119 147 28 308.79 0.51 161 119 148 29 308.77 0.52 162 119 188 69 115.53 0.58 163 119 189 70 114.90 0.88 164 119 191 72 111.80 0.85 165 120 123 3 370.35 1.30 166 120 124 4 370.51 1.39 167 120 147 27 309.62 0.58 168 120 148 28 308.78 0.52 169 120 150 30 296.25 1.93 170 120 188 68 115.53 0.58 171 121 124 3 375.35 3.48 172 121 125 4 365.26 0.90 173 122 125 3 365.35 0.93 174 122 126 4 364.77 1.06 175 123 126 3 368.82 0.95 176 123 127 4 363.89 1.51 177 123 146 23 309.66 0.58 178 123 147 24 309.62 0.58 179 123 149 26 295.62 1.59 180 124 127 3 365.06 0.39 181 124 128 4 361.02 0.10 182 124 149 25 301.65 0.70 183 124 150 26 295.51 1.56 184 124 151 27 278.57 1.11 185 125 128 3 356.67 0.98 186 125 129 4 354.66 0.11 187 126 129 3 363.99 0.22 188 126 130 4 340.95 1.33 189 126 146 20 309.67 0.59 190 127 130 3 359.31 7.84 191 127 131 4 340.94 1.32 192 127 149 22 300.08 0.86 193 127 155 28 214.40 1.20 194 127 159 32 213.75 1.15 195 128 131 3 370.17 2.41 196 128 132 4 359.28 7.85 197 129 132 3 369.96 2.52 198 129 133 4 353.28 10.85 199 130 133 3 360.68 7.16 200 130 138 8 310.09 0.52 201 130 141 11 310.03 0.53 202 130 144 14 309.83 0.56 203 130 159 29 213.75 1.15 204 130 162 32 213.63 1.16 205 131 160 29 213.75 1.15 206 131 161 30 213.66 1.16 207 133 137 4 347.50 8.41 208 133 138 5 321.59 2.54 209 133 141 8 310.16 0.55 210 134 137 3 378.81 3.88 211 134 138 4 366.85 1.29 212 135 138 3 367.97 0.76 213 135 139 4 366.88 1.30 214 136 139 3 378.21 3.47 215 136 140 4 372.81 0.77 216 137 140 3 372.24 0.48 217 137 141 4 367.88 2.04 218 138 141 3 376.19 1.54 219 138 161 23 213.64 1.16 220 138 162 24 213.61 1.15 221 139 166 27 213.02 0.94 222 141 144 3 411.86 0.67 223 141 162 21 213.61 1.15 224 141 166 25 212.77 1.05 225 142 166 24 212.59 0.97 226 142 206 64 86.23 0.46 227 142 207 65 86.22 0.47 228 142 210 68 70.69 1.24 229 143 162 19 213.62 1.16 230 143 166 23 212.55 0.99 231 143 202 59 105.38 0.52 232 143 203 60 102.68 0.57 233 143 206 63 86.48 0.34 234 144 159 15 213.75 1.15 235 144 162 18 213.62 1.15 236 144 166 22 212.83 1.05 237 144 167 23 212.54 0.99 238 144 168 24 212.24 1.11 239 144 202 58 105.71 0.65 240 145 168 23 212.22 1.11 241 145 170 25 212.00 1.19 242 145 199 54 105.75 0.65 243 145 202 57 105.72 0.64 244 145 203 58 105.41 0.50 245 146 149 3 381.45 3.10 246 146 159 13 213.75 1.15 247 146 167 21 212.85 1.04 248 146 168 22 212.63 0.96 249 146 169 23 212.12 1.16 250 146 170 24 211.20 0.78 251 147 170 23 210.95 0.83 252 147 191 44 111.81 0.85 253 147 194 47 106.91 0.53 254 147 195 48 107.15 0.41 255 147 199 52 106.58 0.66 256 148 170 22 212.18 1.10 257 148 171 23 210.95 0.84 258 148 177 29 209.53 0.93 259 148 178 30 210.01 0.55 260 148 188 40 115.53 0.58 261 148 191 43 113.56 0.43 262 149 152 3 365.73 0.02 263 149 155 6 254.10 3.14 264 149 158 9 214.28 0.99 265 149 169 20 212.76 1.01 266 149 171 22 211.78 1.06 267 149 177 28 209.41 0.88 268 149 178 29 209.37 0.85 269 150 154 4 378.54 0.53 270 150 177 27 209.41 0.88 271 151 154 3 371.61 0.74 272 151 155 4 279.00 15.58 273 152 156 4 254.12 3.14 274 152 157 5 214.30 0.98 275 152 169 17 213.06 0.97 276 152 171 19 212.78 1.01 277 152 178 26 209.38 0.86 278 153 156 3 372.76 1.33 279 153 178 25 211.15 0.76 280 153 179 26 209.38 0.86 281 153 180 27 209.31 0.88 282 154 180 26 208.74 0.60 283 155 158 3 373.48 0.21 284 155 160 5 214.41 0.95 285 157 169 12 213.09 0.96 286 158 162 4 352.20 8.36 287 158 164 6 213.64 1.13 288 159 162 3 369.23 2.02 289 159 167 8 213.09 0.96 290 162 166 4 363.81 0.58 291 162 167 5 322.13 4.53 292 163 166 3 375.18 1.98 293 163 167 4 348.26 8.35 294 164 167 3 349.85 7.56 295 165 202 37 105.78 0.67 296 165 206 41 102.16 0.85 297 166 202 36 105.75 0.66 298 166 206 40 95.88 0.72 299 166 210 44 86.26 0.48 300 167 202 35 105.77 0.66 301 168 202 34 105.77 0.66 302 170 191 21 114.00 0.54 303 170 194 24 107.28 0.37 304 170 198 28 107.25 0.35 305 170 199 29 106.69 0.62 306 171 191 20 114.86 0.88 307 172 187 15 121.20 1.06 308 172 190 18 120.04 0.66 309 172 191 19 117.98 0.36 310 172 194 22 114.06 0.54 311 173 187 14 125.95 1.27 312 174 187 13 129.58 0.54 313 175 187 12 121.61 0.91 314 175 188 13 121.53 0.95 315 175 191 16 121.50 0.94 316 176 181 5 495.48 8.72 317 176 183 7 328.56 7.98 318 176 185 9 145.56 6.91 319 177 181 4 404.91 0.58 320 177 182 5 355.22 5.34 321 177 184 7 130.40 0.17 322 177 188 11 121.59 0.90 323 178 191 13 121.37 0.89 324 184 188 4 339.53 1.08 325 184 189 5 353.59 8.11 326 185 188 3 376.42 2.19 327 186 189 3 377.38 1.70 328 186 190 4 375.87 2.46 329 187 190 3 379.13 0.83 330 187 191 4 380.62 0.55 331 188 191 3 406.21 0.15 332 190 193 3 468.50 0.40 333 191 194 3 381.89 3.46 334 191 195 4 353.24 6.84 335 192 195 3 371.19 2.12 336 192 196 4 353.25 6.85 337 193 196 3 353.25 6.85 338 193 197 4 353.25 6.85 339 193 198 5 351.96 7.48 340 194 197 3 353.97 6.49 341 194 198 4 329.04 3.81 342 194 199 5 328.50 4.07 343 194 200 6 328.55 4.05 344 195 199 4 328.49 4.07 345 195 200 5 328.53 4.04 346 196 200 4 340.86 0.13 347 197 200 3 373.67 3.25 348 197 201 4 328.88 3.84 349 198 201 3 338.91 0.84 350 198 202 4 338.91 0.85 351 199 202 3 351.80 7.29 352 199 203 4 338.45 1.09 353 200 203 3 338.45 1.09 354 200 204 4 338.45 1.09 355 201 204 3 371.33 1.35 356 201 205 4 337.96 1.34 357 202 205 3 344.09 4.55 358 202 206 4 334.64 0.34 359 203 206 3 350.22 7.43 360 203 207 4 350.36 7.36 361 204 207 3 353.78 5.65 362 204 208 4 334.82 0.42 363 205 208 3 350.94 7.08 364 205 209 4 342.08 3.20 365 206 209 3 374.21 2.07 366 206 210 4 359.57 5.55 367 207 210 3 378.76 2.96 368 207 211 4 334.76 0.46 369 208 211 3 359.28 12.71 370 208 212 4 296.51 18.68