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 1 46 45 68.12 0.96 2 1 132 131 68.06 0.96 3 2 43 41 68.20 0.94 4 2 44 42 68.18 0.94 5 2 46 44 68.17 0.95 6 2 47 45 68.17 0.95 7 2 69 67 68.11 0.96 8 2 72 70 68.12 0.96 9 2 131 129 68.11 0.97 10 2 132 130 68.06 0.96 11 2 134 132 68.10 0.96 12 3 41 38 68.22 0.94 13 3 42 39 68.20 0.94 14 3 43 40 68.20 0.95 15 3 132 129 68.13 0.96 16 3 133 130 68.11 0.96 17 3 134 131 68.10 0.96 18 4 41 37 68.25 0.93 19 4 42 38 68.20 0.94 20 4 44 40 68.25 0.93 21 4 67 63 68.12 0.96 22 4 68 64 68.17 0.95 23 4 69 65 68.17 0.95 24 4 126 122 68.10 0.96 25 4 134 130 68.11 0.96 26 5 39 34 73.98 1.56 27 5 40 35 73.55 1.72 28 5 41 36 68.25 0.93 29 5 134 129 68.14 0.96 30 5 135 130 68.11 0.97 31 5 136 131 68.11 0.96 32 6 33 27 74.06 1.58 33 6 39 33 74.04 1.57 34 6 40 34 73.55 1.72 35 6 53 47 73.53 1.72 36 6 67 61 68.22 0.95 37 6 136 130 68.11 0.97 38 6 138 132 68.09 0.96 39 7 39 32 74.06 1.56 40 7 136 129 68.14 0.96 41 7 137 130 68.11 0.97 42 7 138 131 68.11 0.97 43 8 40 32 74.14 1.53 44 8 55 47 74.30 1.60 45 8 138 130 68.11 0.97 46 8 140 132 68.09 0.97 47 9 137 128 68.15 0.96 48 9 138 129 68.12 0.96 49 9 139 130 68.11 0.96 50 9 140 131 68.10 0.97 51 10 16 6 83.17 1.38 52 10 17 7 81.09 0.58 53 10 140 130 68.11 0.97 54 11 139 128 68.14 0.96 55 11 140 129 68.11 0.96 56 11 141 130 68.11 0.97 57 12 15 3 496.57 4.09 58 12 120 108 89.95 1.67 59 12 141 129 68.11 0.96 60 14 120 106 104.92 2.45 61 15 57 42 300.36 23.39 62 15 59 44 300.55 23.53 63 15 120 105 112.25 1.20 64 16 57 41 300.74 23.57 65 17 55 38 300.42 23.43 66 17 56 39 301.11 23.39 67 17 57 40 301.12 23.39 68 17 61 44 302.05 23.86 69 17 62 45 300.74 23.58 70 17 63 46 300.74 23.57 71 17 120 103 130.34 0.35 72 17 122 105 126.66 0.93 73 17 140 123 68.09 0.96 74 18 55 37 301.11 23.39 75 18 56 38 302.24 23.93 76 19 40 21 307.68 26.39 77 19 54 35 301.75 23.70 78 19 55 36 301.97 23.81 79 20 54 34 302.57 24.03 80 20 55 35 302.69 23.96 81 20 56 36 302.66 23.96 82 21 53 32 302.81 23.94 83 21 54 33 302.70 23.97 84 21 87 66 255.58 0.42 85 21 88 67 255.25 0.27 86 21 89 68 255.44 0.36 87 22 33 11 308.70 26.11 88 22 40 18 308.07 26.37 89 22 52 30 302.90 23.94 90 22 53 31 302.83 23.93 91 23 33 10 309.65 25.71 92 23 51 28 303.58 23.76 93 23 52 29 302.98 23.91 94 23 88 65 255.73 0.40 95 23 89 66 255.66 0.39 96 23 92 69 255.49 0.30 97 24 30 6 318.12 21.50 98 24 31 7 311.00 25.06 99 24 32 8 311.00 25.05 100 24 33 9 309.69 25.71 101 24 42 18 309.68 25.70 102 24 50 26 304.70 24.28 103 24 51 27 303.60 23.75 104 24 92 68 255.71 0.41 105 25 30 5 331.45 14.84 106 25 49 24 305.70 23.84 107 25 50 25 305.08 24.10 108 25 92 67 255.72 0.41 109 25 93 68 255.66 0.39 110 25 96 71 254.84 0.21 111 27 30 3 467.69 1.50 112 27 48 21 323.75 17.95 113 27 49 22 317.47 19.64 114 27 96 69 255.44 0.41 115 28 45 17 329.60 15.72 116 28 46 18 327.42 16.80 117 28 47 19 327.41 16.79 118 28 48 20 326.06 17.11 119 28 49 21 325.11 16.64 120 29 45 16 329.74 15.64 121 30 44 14 329.89 15.59 122 30 45 15 329.85 15.59 123 30 49 19 325.93 13.76 124 31 43 12 329.99 15.54 125 31 44 13 329.87 15.56 126 32 41 9 331.74 16.06 127 32 42 10 331.47 15.99 128 32 43 11 330.60 15.79 129 33 40 7 334.06 14.95 130 33 41 8 331.74 16.06 131 33 42 9 331.67 16.09 132 33 51 18 326.18 13.62 133 33 52 19 326.18 13.62 134 33 53 20 326.06 13.61 135 33 67 34 324.87 12.91 136 34 40 6 334.81 14.58 137 34 41 7 331.86 16.02 138 35 38 3 471.19 2.50 139 35 39 4 415.41 5.40 140 35 40 5 346.04 8.96 141 36 39 3 459.78 3.02 142 36 41 5 407.22 1.30 143 40 53 13 325.88 13.47 144 42 50 8 329.00 12.23 145 42 51 9 326.25 13.59 146 42 67 25 324.91 12.88 147 44 49 5 339.69 11.49 148 44 50 6 329.96 11.79 149 44 68 24 329.22 10.73 150 44 69 25 351.43 0.39 151 47 69 22 374.61 11.98 152 47 71 24 374.64 12.05 153 47 72 25 371.57 13.59 154 48 69 21 374.71 12.04 155 49 68 19 374.86 12.11 156 49 69 20 374.81 12.12 157 49 96 47 255.31 0.42 158 50 66 16 375.10 12.21 159 50 67 17 374.99 12.17 160 50 68 18 374.61 12.23 161 50 75 25 332.76 33.09 162 50 92 42 255.74 0.39 163 50 96 46 254.82 0.20 164 51 66 15 375.08 12.22 165 51 67 16 375.03 12.22 166 51 92 41 255.68 0.38 167 52 64 12 375.19 12.25 168 52 65 13 375.13 12.25 169 52 66 14 374.99 12.29 170 52 88 36 255.74 0.37 171 52 91 39 255.72 0.37 172 52 92 40 255.44 0.27 173 53 64 11 375.19 12.29 174 53 65 12 375.14 12.27 175 53 67 14 375.10 12.29 176 54 63 9 375.27 12.27 177 54 64 10 375.11 12.34 178 54 82 28 327.76 35.51 179 54 87 33 255.75 0.35 180 54 88 34 255.41 0.23 181 55 62 7 375.38 12.22 182 55 63 8 375.38 12.22 183 55 138 83 68.16 0.96 184 56 60 4 445.23 1.72 185 56 61 5 391.35 4.30 186 56 62 6 375.39 12.21 187 57 60 3 464.63 4.16 188 57 61 4 397.73 1.11 189 59 120 61 146.15 0.70 190 61 116 55 146.73 0.82 191 61 118 57 146.14 0.69 192 61 120 59 146.09 0.68 193 62 80 18 327.83 35.54 194 62 81 19 327.74 35.53 195 62 82 20 327.70 35.54 196 63 78 15 327.90 35.53 197 63 79 16 327.82 35.52 198 63 80 17 327.78 35.51 199 63 82 19 327.72 35.53 200 63 122 59 140.86 0.24 201 63 138 75 68.17 0.96 202 63 140 77 68.10 0.97 203 64 78 14 327.85 35.50 204 64 79 15 327.81 35.51 205 64 82 18 327.37 35.33 206 64 88 24 255.60 0.28 207 64 91 27 255.58 0.29 208 65 77 12 327.94 35.47 209 65 78 13 327.83 35.49 210 65 124 59 140.50 0.21 211 65 138 73 68.09 0.97 212 66 75 9 388.03 5.50 213 66 76 10 327.99 35.43 214 66 77 11 327.98 35.44 215 66 95 29 255.07 0.07 216 67 75 8 387.98 5.48 217 67 76 9 327.99 35.43 218 67 124 57 140.69 0.21 219 67 126 59 140.05 0.42 220 67 136 69 68.14 0.96 221 68 74 6 388.25 5.45 222 68 75 7 388.07 5.43 223 69 72 3 467.94 0.58 224 69 73 4 408.47 2.70 225 69 74 5 395.16 3.62 226 69 75 6 388.26 5.45 227 69 134 65 83.19 1.44 228 70 73 3 463.56 1.61 229 70 75 5 404.19 1.95 230 70 105 35 187.23 0.74 231 70 106 36 186.50 0.39 232 70 108 38 185.63 0.57 233 71 108 37 186.16 0.54 234 73 108 35 185.75 0.58 235 73 130 57 116.42 0.65 236 74 108 34 184.44 0.04 237 74 109 35 184.43 0.04 238 74 110 36 177.38 0.78 239 74 126 52 140.27 0.34 240 74 129 55 113.13 0.58 241 74 130 56 113.00 0.65 242 74 134 60 82.95 1.32 243 75 95 20 255.58 0.29 244 75 96 21 255.58 0.29 245 75 105 30 186.28 0.61 246 75 108 33 177.59 0.83 247 75 109 34 174.59 0.58 248 75 126 51 140.60 0.18 249 76 109 33 173.10 1.31 250 76 111 35 158.32 0.96 251 76 112 36 147.72 0.53 252 76 124 48 140.72 0.21 253 76 126 50 140.61 0.17 254 77 95 18 254.72 0.14 255 77 104 27 186.11 0.43 256 77 112 35 147.63 0.57 257 77 124 47 140.78 0.21 258 78 112 34 147.63 0.57 259 78 113 35 147.56 0.56 260 78 114 36 147.36 0.57 261 78 122 44 143.38 0.24 262 78 123 45 140.84 0.23 263 78 124 46 140.76 0.21 264 78 138 60 68.15 0.96 265 79 82 3 514.61 1.48 266 79 91 12 255.62 0.27 267 79 95 16 254.59 0.21 268 79 101 22 186.58 0.52 269 80 114 34 147.23 0.62 270 80 116 36 146.23 0.62 271 80 122 42 145.06 0.98 272 81 116 35 146.34 0.51 273 81 117 36 146.18 0.58 274 82 86 4 425.96 5.66 275 82 91 9 396.67 1.73 276 83 86 3 469.88 0.72 277 84 87 3 494.79 0.95 278 85 90 5 451.67 1.22 279 86 90 4 451.67 1.22 280 86 91 5 451.53 1.15 281 87 90 3 468.69 0.44 282 87 91 4 467.03 0.70 283 88 91 3 467.03 0.70 284 88 92 4 465.54 1.44 285 89 92 3 467.03 0.69 286 89 93 4 467.19 0.61 287 90 93 3 477.45 2.06 288 90 94 4 471.78 2.90 289 91 94 3 473.55 2.02 290 91 95 4 472.51 2.54 291 91 101 10 411.80 4.62 292 92 95 3 477.61 3.00 293 92 96 4 477.30 0.15 294 93 96 3 479.31 1.16 295 93 97 4 470.09 3.75 296 94 97 3 463.92 0.66 297 94 98 4 448.21 4.54 298 94 101 7 417.66 1.69 299 95 101 6 411.81 4.62 300 95 102 7 412.49 1.56 301 95 105 10 405.46 1.95 302 96 102 6 419.06 1.72 303 96 105 9 411.89 1.20 304 97 102 5 444.57 3.56 305 98 101 3 465.86 1.20 306 98 102 4 452.26 0.23 307 99 102 3 462.60 0.61 308 99 103 4 458.10 2.69 309 100 103 3 469.94 1.45 310 100 104 4 459.87 0.80 311 101 104 3 462.67 2.19 312 101 105 4 459.87 0.80 313 102 105 3 468.14 2.33 314 102 106 4 459.86 0.80 315 103 106 3 460.88 1.30 316 103 107 4 455.17 1.55 317 104 107 3 464.97 1.78 318 105 108 3 469.88 1.48 319 109 112 3 484.94 0.25 320 109 126 17 140.74 0.18 321 110 125 15 140.80 0.20 322 110 126 16 140.69 0.20 323 110 129 19 114.45 1.09 324 111 124 13 140.84 0.21 325 111 125 14 140.78 0.21 326 112 123 11 143.75 0.59 327 112 124 12 140.83 0.21 328 113 121 8 145.40 1.07 329 113 122 9 145.19 1.01 330 113 123 10 144.13 0.61 331 114 121 7 146.02 0.74 332 114 122 8 145.33 1.06 333 115 119 4 407.98 3.10 334 115 120 5 261.38 52.83 335 115 121 6 145.97 0.77 336 116 119 3 450.16 1.82 337 116 120 4 405.08 1.67 338 116 122 6 261.38 52.81 339 120 140 20 68.17 0.96 340 120 141 21 68.10 0.96 341 121 140 19 68.16 0.96 342 121 141 20 68.09 0.96 343 122 139 17 68.16 0.96 344 122 140 18 68.09 0.96 345 123 138 15 68.16 0.96 346 123 139 16 68.12 0.96 347 124 136 12 68.20 0.95 348 124 137 13 68.16 0.96 349 124 138 14 68.12 0.96 350 125 136 11 68.20 0.95 351 125 137 12 68.17 0.96 352 125 139 14 68.14 0.96 353 126 129 3 443.93 0.23 354 126 134 8 82.38 1.35 355 126 135 9 76.41 3.15 356 126 136 10 68.14 0.96 357 127 135 8 82.20 1.28 358 127 136 9 76.97 3.44 359 127 137 10 76.97 3.44 360 128 133 5 422.09 3.72 361 128 134 6 119.40 15.95 362 128 135 7 82.31 1.30 363 129 134 5 268.09 55.75 364 130 134 4 427.96 0.80 365 131 134 3 500.50 2.78