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 2 120 118 32.27 0.87 2 2 121 119 32.27 0.87 3 2 124 122 32.42 0.94 4 2 135 133 32.27 0.88 5 2 138 136 32.23 0.88 6 2 139 137 32.23 0.88 7 2 142 140 32.23 0.88 8 3 8 5 432.81 10.48 9 3 139 136 32.27 0.88 10 3 142 139 32.24 0.88 11 3 143 140 32.24 0.88 12 4 117 113 32.28 0.88 13 4 142 138 32.24 0.88 14 4 143 139 32.23 0.88 15 4 146 142 32.23 0.88 16 5 143 138 32.27 0.87 17 6 143 137 32.39 0.93 18 8 136 128 41.02 0.83 19 8 139 131 35.17 1.45 20 8 140 132 32.62 0.93 21 8 143 135 32.61 0.93 22 9 136 127 49.61 1.26 23 10 136 126 50.11 1.09 24 11 15 4 497.06 0.07 25 11 16 5 491.00 0.70 26 11 88 77 54.05 0.14 27 11 133 122 55.99 0.09 28 11 136 125 50.13 1.09 29 11 137 126 50.11 1.08 30 11 140 129 50.11 1.08 31 12 15 3 507.56 5.33 32 12 16 4 504.93 4.00 33 13 16 3 507.67 5.37 34 13 17 4 500.22 1.64 35 14 17 3 516.58 0.83 36 14 18 4 501.37 2.21 37 15 18 3 509.90 2.04 38 15 19 4 499.27 2.11 39 15 133 118 76.75 0.25 40 15 136 121 77.75 0.25 41 16 19 3 499.26 2.10 42 16 20 4 499.27 2.08 43 16 88 72 78.28 0.06 44 16 89 73 80.52 1.17 45 17 20 3 508.06 2.29 46 17 21 4 508.06 2.31 47 18 21 3 509.03 2.79 48 18 22 4 505.68 3.50 49 18 128 110 97.60 0.31 50 18 131 113 96.81 0.71 51 19 22 3 512.28 1.29 52 19 23 4 505.68 3.50 53 19 85 66 96.75 0.70 54 19 88 69 96.78 0.70 55 19 133 114 96.78 0.70 56 19 134 115 96.75 0.70 57 19 137 118 96.76 0.70 58 20 23 3 516.48 0.83 59 20 24 4 505.44 3.61 60 20 85 65 96.78 0.70 61 20 88 68 97.13 0.53 62 20 89 69 97.39 0.48 63 21 24 3 518.92 2.06 64 21 25 4 519.66 1.69 65 22 25 3 528.96 1.33 66 22 26 4 517.26 0.49 67 22 127 105 104.44 2.43 68 22 128 106 104.42 2.42 69 23 26 3 519.66 1.69 70 23 27 4 505.34 2.35 71 23 78 55 104.45 2.42 72 23 81 58 104.42 2.43 73 23 82 59 104.44 2.43 74 23 85 62 104.39 2.43 75 23 123 100 104.45 2.43 76 23 127 104 104.45 2.43 77 23 134 111 104.45 2.43 78 24 27 3 513.95 4.50 79 24 28 4 497.92 0.19 80 25 28 3 506.59 0.20 81 25 29 4 502.54 2.50 82 26 29 3 519.62 1.66 83 26 30 4 502.51 2.51 84 26 33 7 381.32 12.75 85 26 127 101 104.64 2.46 86 27 30 3 494.15 1.70 87 27 79 52 105.31 2.11 88 27 82 55 104.58 2.46 89 29 32 3 518.02 1.85 90 29 33 4 450.14 2.93 91 30 33 3 480.45 2.75 92 30 34 4 462.28 10.76 93 30 75 45 169.41 20.29 94 30 78 48 125.70 0.32 95 30 79 49 168.12 20.90 96 31 35 4 493.95 1.80 97 31 75 44 169.41 20.29 98 32 35 3 504.66 2.66 99 32 36 4 493.95 1.80 100 33 36 3 507.75 1.84 101 33 37 4 500.14 1.17 102 34 37 3 512.73 0.65 103 34 38 4 500.94 0.77 104 34 74 40 181.44 14.73 105 34 78 44 177.15 16.68 106 35 38 3 504.91 2.75 107 35 39 4 494.87 2.27 108 35 65 30 198.15 14.96 109 35 71 36 189.66 11.10 110 35 74 39 186.61 12.16 111 36 39 3 505.12 2.83 112 36 40 4 492.15 3.63 113 36 65 29 198.19 14.98 114 37 40 3 505.06 2.77 115 37 41 4 494.90 1.47 116 37 78 41 188.78 10.87 117 37 119 82 170.30 1.79 118 37 122 85 170.13 1.67 119 37 123 86 170.11 1.68 120 37 126 89 170.15 1.66 121 38 41 3 506.75 1.93 122 38 42 4 497.06 0.30 123 38 52 14 215.69 20.82 124 38 55 17 207.78 19.50 125 38 70 32 196.08 14.16 126 38 73 35 190.91 11.68 127 38 74 36 190.74 11.70 128 38 77 39 190.71 11.71 129 38 119 81 170.40 1.74 130 39 42 3 503.80 3.10 131 39 43 4 497.04 0.29 132 39 61 22 199.02 15.18 133 39 64 25 198.30 15.02 134 39 65 26 198.31 15.02 135 39 70 31 196.83 14.52 136 40 43 3 504.38 3.38 137 40 44 4 494.76 1.41 138 40 122 82 170.31 1.63 139 41 44 3 512.50 1.21 140 41 45 4 494.76 1.41 141 41 48 7 441.38 6.50 142 41 52 11 290.07 21.17 143 41 115 74 170.71 1.93 144 41 118 77 170.71 1.92 145 41 119 78 170.41 1.75 146 41 122 81 170.31 1.62 147 42 45 3 512.63 1.14 148 42 49 7 367.24 6.12 149 42 52 10 286.45 19.38 150 42 55 13 214.95 20.45 151 42 59 17 201.75 16.31 152 42 64 22 199.16 15.16 153 43 46 3 525.33 0.10 154 43 49 6 446.85 9.26 155 43 64 21 199.16 15.15 156 45 48 3 512.19 2.26 157 45 49 4 512.22 1.47 158 45 115 70 170.85 1.90 159 45 118 73 170.88 1.89 160 46 49 3 516.48 0.12 161 47 51 4 525.72 0.45 162 47 115 68 170.94 1.91 163 48 51 3 524.88 0.38 164 48 52 4 515.71 0.27 165 48 115 67 170.91 1.92 166 49 52 3 515.70 0.28 167 49 59 10 208.69 19.56 168 51 110 59 170.51 2.16 169 51 111 60 170.50 2.16 170 51 112 61 170.75 2.06 171 51 115 64 170.99 1.92 172 52 55 3 508.06 0.79 173 52 56 4 501.34 0.53 174 52 73 21 199.31 15.06 175 53 56 3 507.68 1.06 176 54 58 4 538.82 1.57 177 54 69 15 202.55 16.48 178 55 58 3 524.86 4.40 179 55 69 14 202.56 16.48 180 55 70 15 202.53 16.48 181 55 73 18 202.56 16.48 182 58 63 5 448.96 3.00 183 58 64 6 372.28 9.58 184 58 67 9 250.93 26.30 185 58 70 12 249.61 26.94 186 59 63 4 504.07 1.99 187 60 63 3 515.27 0.60 188 60 64 4 504.10 1.98 189 61 64 3 512.96 1.09 190 61 65 4 504.10 1.98 191 62 65 3 512.07 0.60 192 62 66 4 500.90 0.37 193 63 66 3 505.50 2.68 194 63 67 4 500.17 0.01 195 64 67 3 500.17 0.03 196 64 70 6 443.64 10.93 197 65 71 6 416.12 3.06 198 67 70 3 504.18 3.06 199 67 71 4 498.97 0.45 200 68 71 3 507.54 4.73 201 68 72 4 498.96 0.45 202 69 72 3 498.97 0.46 203 69 73 4 498.95 0.46 204 70 73 3 502.45 2.21 205 70 74 4 489.62 3.58 206 71 74 3 503.73 3.48 207 71 75 4 503.72 3.49 208 72 75 3 505.67 2.52 209 72 76 4 489.72 3.59 210 73 76 3 505.66 2.52 211 73 77 4 491.57 4.51 212 74 77 3 501.73 1.09 213 74 78 4 495.95 3.79 214 75 78 3 504.01 2.50 215 75 79 4 495.95 3.79 216 76 79 3 501.32 3.85 217 76 80 4 496.30 3.62 218 77 80 3 502.97 3.02 219 77 81 4 498.58 2.48 220 77 119 42 171.47 2.17 221 78 81 3 499.58 1.98 222 78 82 4 495.03 2.84 223 79 82 3 497.54 1.57 224 79 83 4 492.79 0.80 225 80 83 3 499.33 0.66 226 80 84 4 493.86 1.30 227 80 101 21 171.71 2.42 228 81 84 3 497.31 0.35 229 81 85 4 493.86 1.31 230 81 123 42 180.69 2.43 231 81 138 57 171.00 1.73 232 81 141 60 170.75 1.82 233 82 85 3 498.62 0.57 234 82 86 4 491.87 1.54 235 83 86 3 498.10 0.82 236 83 87 4 494.41 0.27 237 83 97 14 210.49 14.83 238 84 87 3 506.10 1.03 239 84 88 4 492.47 0.70 240 84 94 10 213.18 16.16 241 84 137 53 182.58 3.90 242 84 141 57 170.84 1.82 243 85 88 3 499.80 2.62 244 85 137 52 182.59 3.90 245 87 90 3 499.26 2.35 246 87 93 6 344.56 1.31 247 87 94 7 246.80 27.42 248 88 94 6 398.82 10.59 249 88 137 49 229.25 27.21 250 90 93 3 499.02 7.80 251 90 94 4 480.70 1.31 252 91 94 3 488.63 2.66 253 91 95 4 480.87 1.39 254 92 96 4 498.40 1.95 255 93 96 3 514.15 1.36 256 93 97 4 498.70 1.82 257 94 97 3 520.35 0.14 258 94 98 4 498.43 1.97 259 94 144 50 255.19 40.34 260 95 98 3 505.96 4.99 261 95 99 4 498.42 1.97 262 95 144 49 255.18 40.35 263 96 99 3 500.15 2.83 264 96 100 4 496.90 1.49 265 97 100 3 496.60 1.64 266 97 101 4 496.60 1.65 267 98 101 3 501.54 0.35 268 98 102 4 496.58 1.65 269 98 141 43 255.94 40.76 270 98 144 46 255.80 40.83 271 98 145 47 255.36 41.05 272 99 102 3 500.68 0.07 273 99 103 4 497.46 1.22 274 99 144 45 255.80 40.84 275 99 147 48 255.22 41.09 276 100 103 3 508.76 1.42 277 100 104 4 497.79 1.38 278 101 104 3 508.73 1.44 279 101 105 4 497.79 1.39 280 101 145 44 255.44 41.19 281 102 105 3 499.62 2.31 282 102 106 4 496.73 1.59 283 102 144 42 255.56 41.16 284 102 145 43 254.69 41.56 285 102 146 44 254.69 41.56 286 102 147 45 254.34 41.74 287 102 148 46 253.71 41.98 288 103 106 3 497.35 1.29 289 103 107 4 467.66 2.76 290 103 148 45 253.84 41.88 291 104 108 4 386.06 20.97 292 104 109 5 357.49 19.10 293 105 109 4 338.42 11.86 294 105 110 5 327.61 6.46 295 105 111 6 310.44 13.98 296 105 116 11 300.78 18.64 297 105 149 44 253.81 42.04 298 106 110 4 338.41 11.88 299 106 148 42 253.83 42.04 300 106 149 43 253.55 42.15 301 111 116 5 496.92 0.99 302 111 149 38 263.70 37.25 303 112 115 3 525.73 0.95 304 113 116 3 528.10 1.06 305 113 146 33 267.16 35.54 306 113 149 36 265.51 36.34 307 114 117 3 540.77 1.60 308 114 118 4 512.03 0.65 309 114 146 32 267.54 35.62 310 115 118 3 508.06 1.34 311 115 119 4 502.84 3.96 312 116 119 3 508.21 1.42 313 116 120 4 494.28 0.32 314 116 142 26 267.73 35.62 315 116 145 29 267.74 35.61 316 116 146 30 267.69 35.60 317 116 149 33 267.67 35.58 318 117 120 3 502.82 3.95 319 117 121 4 494.29 0.32 320 117 142 25 267.80 35.62 321 118 121 3 514.78 0.67 322 118 122 4 493.86 0.10 323 119 122 3 499.62 2.79 324 119 123 4 486.41 3.62 325 120 123 3 498.55 0.96 326 120 124 4 480.50 0.69 327 120 138 18 268.15 35.62 328 120 142 22 267.97 35.55 329 121 124 3 474.32 3.77 330 121 125 4 470.69 5.58 331 122 126 4 467.60 2.21 332 123 126 3 501.73 0.14 333 123 127 4 449.87 1.38 334 123 134 11 316.49 11.94 335 123 138 15 269.07 35.57 336 124 127 3 503.16 4.61 337 124 128 4 448.78 0.82 338 124 129 5 360.82 3.10 339 124 134 10 270.20 35.08 340 124 135 11 269.98 35.14 341 124 138 14 269.06 35.58 342 125 129 4 360.82 3.10 343 127 134 7 316.81 12.05 344 128 131 3 512.89 4.58 345 131 134 3 501.29 2.90 346 131 135 4 485.82 9.20 347 132 135 3 485.91 9.18 348 132 136 4 484.78 9.72 349 133 136 3 492.03 6.10 350 133 137 4 492.03 6.10 351 134 137 3 495.17 3.46 352 134 138 4 490.94 5.57 353 135 138 3 491.88 6.03 354 135 139 4 490.94 5.57 355 136 139 3 490.94 5.57 356 136 140 4 490.94 5.57 357 137 140 3 498.82 1.62 358 137 141 4 490.94 5.57 359 138 141 3 483.39 1.80 360 138 142 4 481.91 1.06 361 139 142 3 495.06 0.42 362 139 143 4 488.48 3.56 363 140 143 3 498.28 1.62 364 140 144 4 488.57 3.56 365 141 144 3 507.14 2.81 366 141 145 4 488.57 3.56 367 142 145 3 498.03 1.15 368 142 146 4 491.84 1.92 369 143 146 3 504.40 2.02 370 143 147 4 497.24 1.54 371 144 147 3 502.49 1.06 372 145 149 4 524.79 1.35 373 146 149 3 506.12 2.19