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 7 5 462.69 4.12 2 2 73 71 28.75 0.66 3 2 127 125 24.06 0.21 4 2 128 126 24.00 0.18 5 2 131 129 23.90 0.16 6 3 6 3 466.91 2.09 7 3 7 4 465.14 2.96 8 4 7 3 475.22 2.06 9 4 8 4 467.24 1.92 10 5 8 3 467.25 1.92 11 5 9 4 469.62 0.72 12 6 9 3 469.61 0.71 13 6 10 4 469.61 0.71 14 6 124 118 46.71 0.49 15 6 127 121 46.63 0.45 16 7 10 3 480.26 1.91 17 7 11 4 469.59 0.70 18 7 73 66 46.98 0.61 19 7 74 67 47.31 0.78 20 8 11 3 478.45 0.26 21 8 12 4 472.60 2.21 22 9 12 3 475.75 0.65 23 9 13 4 465.98 0.14 24 9 120 111 64.86 0.26 25 9 121 112 64.59 0.14 26 9 124 115 64.18 0.04 27 10 13 3 471.94 2.56 28 10 14 4 463.11 1.56 29 10 70 60 64.20 0.04 30 10 124 114 64.59 0.13 31 10 125 115 64.56 0.14 32 10 128 118 64.17 0.04 33 11 14 3 479.89 2.15 34 11 15 4 462.64 1.66 35 11 70 59 64.56 0.14 36 11 73 62 64.58 0.13 37 12 15 3 477.92 2.45 38 12 16 4 470.10 3.56 39 13 16 3 481.68 2.64 40 13 17 4 470.11 3.56 41 13 113 100 79.71 0.89 42 13 121 108 73.59 0.04 43 13 125 112 70.84 1.31 44 14 17 3 475.80 0.72 45 14 18 4 470.11 3.56 46 14 21 7 380.88 4.93 47 14 63 49 78.11 1.59 48 14 66 52 70.87 1.32 49 14 67 53 70.87 1.32 50 14 70 56 70.83 1.32 51 14 109 95 78.84 1.23 52 15 18 3 470.10 3.56 53 16 113 97 87.03 1.34 54 16 116 100 85.64 1.90 55 17 20 3 487.11 0.20 56 17 21 4 455.31 3.81 57 17 24 7 380.29 5.21 58 17 109 92 85.78 1.97 59 17 113 96 91.39 2.87 60 18 21 3 495.07 1.53 61 20 23 3 477.68 3.95 62 20 24 4 464.03 0.58 63 21 24 3 469.39 0.64 64 21 25 4 464.04 0.58 65 21 63 42 92.36 2.98 66 22 25 3 470.54 3.83 67 22 26 4 468.85 2.98 68 22 59 37 104.50 0.98 69 22 60 38 102.36 2.00 70 22 63 41 99.50 0.58 71 23 26 3 474.07 2.00 72 23 27 4 471.71 1.72 73 24 27 3 477.34 0.36 74 24 28 4 471.71 1.71 75 24 108 84 126.67 1.60 76 24 109 85 129.10 0.39 77 24 112 88 134.05 1.89 78 25 28 3 481.94 1.95 79 25 29 4 471.72 1.72 80 25 59 34 125.78 1.95 81 25 105 80 125.88 2.00 82 26 29 3 481.52 1.72 83 26 30 4 471.64 1.75 84 26 55 29 134.09 3.18 85 26 56 30 131.68 1.97 86 26 59 33 125.83 1.96 87 27 30 3 471.42 1.64 88 27 31 4 473.85 0.42 89 27 108 81 135.74 2.58 90 27 112 85 136.66 2.42 91 28 31 3 473.85 0.42 92 28 32 4 471.18 1.76 93 28 101 73 135.59 2.59 94 28 104 76 135.62 2.58 95 28 105 77 135.60 2.56 96 28 108 80 135.81 2.56 97 29 32 3 473.85 0.42 98 29 33 4 471.18 1.76 99 29 43 14 197.88 27.70 100 29 55 26 136.36 2.85 101 29 58 29 136.03 2.73 102 29 62 33 135.69 2.56 103 29 101 72 135.74 2.60 104 30 33 3 474.09 0.54 105 30 34 4 468.16 0.26 106 30 50 20 137.45 2.51 107 31 34 3 477.32 1.65 108 31 35 4 466.76 0.38 109 31 104 73 137.05 2.54 110 31 107 76 137.19 2.48 111 31 108 77 137.19 2.48 112 31 111 80 137.33 2.48 113 32 35 3 473.72 0.66 114 32 36 4 455.60 0.41 115 32 39 7 351.76 16.91 116 32 100 68 137.14 2.54 117 32 101 69 137.16 2.54 118 32 104 72 137.12 2.50 119 33 37 4 458.01 0.81 120 33 39 6 320.00 1.02 121 33 40 7 264.17 0.56 122 33 43 10 256.56 3.25 123 33 48 15 137.56 2.56 124 33 55 22 137.50 2.54 125 34 37 3 484.37 0.63 126 36 39 3 484.86 0.32 127 36 100 64 137.25 2.56 128 36 103 67 137.38 2.51 129 36 104 68 137.39 2.51 130 37 40 3 479.15 4.38 131 38 41 3 485.37 1.28 132 39 42 3 492.59 4.88 133 39 97 58 137.24 2.56 134 39 100 61 137.38 2.52 135 40 43 3 480.87 0.37 136 40 48 8 252.33 0.42 137 41 44 3 498.91 3.48 138 42 92 50 137.51 2.69 139 42 93 51 137.52 2.69 140 42 94 52 137.53 2.69 141 42 97 55 137.58 2.66 142 43 46 3 487.19 5.46 143 43 48 5 422.27 4.01 144 43 58 15 242.54 3.13 145 45 54 9 270.06 0.22 146 46 54 8 270.01 0.24 147 46 55 9 270.01 0.25 148 46 58 12 270.00 0.24 149 47 52 5 322.16 17.01 150 47 54 7 270.08 0.21 151 47 55 8 270.08 0.21 152 48 52 4 420.53 14.07 153 48 55 7 270.10 0.21 154 49 52 3 482.86 0.04 155 51 56 5 453.94 1.24 156 52 55 3 480.07 4.29 157 52 56 4 453.96 1.23 158 53 56 3 470.07 2.56 159 53 57 4 471.44 0.02 160 54 57 3 482.94 5.70 161 54 58 4 463.84 3.81 162 55 58 3 465.85 2.85 163 55 59 4 467.38 2.04 164 56 59 3 482.94 5.70 165 56 60 4 469.03 1.23 166 57 60 3 474.25 1.42 167 57 61 4 466.12 0.23 168 58 61 3 474.92 1.08 169 58 62 4 468.24 0.83 170 59 62 3 481.56 0.01 171 59 63 4 469.00 1.90 172 60 63 3 482.69 0.66 173 60 64 4 478.16 1.60 174 61 64 3 484.06 1.33 175 61 65 4 478.17 1.61 176 62 65 3 492.83 3.05 177 62 66 4 478.16 1.61 178 62 101 39 150.35 4.42 179 63 66 3 486.94 6.00 180 63 67 4 467.48 1.18 181 64 67 3 486.02 6.46 182 64 68 4 461.99 3.17 183 65 68 3 470.72 1.20 184 65 69 4 461.98 3.17 185 65 83 18 146.21 2.56 186 66 69 3 475.42 3.54 187 66 70 4 461.99 3.17 188 66 105 39 182.83 0.39 189 66 128 62 183.00 0.30 190 66 129 63 177.16 2.44 191 66 132 66 156.81 5.71 192 67 70 3 467.19 0.56 193 67 71 4 460.10 4.09 194 68 71 3 467.79 0.70 195 68 72 4 457.81 2.95 196 68 79 11 190.78 14.52 197 69 72 3 460.50 4.34 198 69 73 4 451.19 0.32 199 69 76 7 260.49 3.04 200 69 80 11 181.70 9.98 201 69 128 59 188.34 2.20 202 69 132 63 169.02 1.30 203 70 73 3 459.07 2.33 204 70 128 58 201.23 4.25 205 72 75 3 472.91 4.62 206 72 76 4 428.56 9.47 207 72 79 7 284.08 5.44 208 73 76 3 485.22 1.53 209 73 128 55 203.47 4.67 210 75 78 3 487.76 0.27 211 75 79 4 473.67 3.52 212 76 79 3 473.13 3.79 213 76 80 4 463.81 0.12 214 76 128 52 205.57 5.01 215 76 131 55 204.28 4.41 216 76 132 56 204.22 4.44 217 76 135 59 204.21 4.44 218 77 80 3 480.10 2.81 219 77 81 4 457.45 3.20 220 77 135 58 204.22 4.43 221 78 81 3 461.48 1.29 222 80 83 3 469.87 1.29 223 80 84 4 466.39 1.11 224 80 132 52 205.74 5.08 225 80 135 55 205.12 4.83 226 80 136 56 205.14 4.82 227 81 84 3 474.54 2.71 228 81 85 4 467.54 0.54 229 82 85 3 474.57 2.73 230 82 86 4 469.49 1.51 231 83 86 3 470.81 0.85 232 83 87 4 468.19 0.24 233 83 136 53 205.77 5.08 234 84 87 3 478.94 3.21 235 84 88 4 466.16 1.14 236 84 135 51 205.78 5.08 237 84 136 52 205.75 5.08 238 84 139 55 205.46 4.95 239 85 88 3 474.88 1.17 240 85 89 4 460.47 0.75 241 86 89 3 479.97 2.73 242 86 90 4 446.45 2.50 243 86 91 5 432.53 4.42 244 87 91 4 402.81 10.43 245 87 92 5 356.76 1.18 246 87 93 6 356.75 1.18 247 87 98 11 276.00 6.11 248 87 136 49 205.91 5.12 249 87 140 53 205.51 4.96 250 88 92 4 400.06 9.05 251 88 139 51 205.78 5.09 252 88 140 52 205.50 4.96 253 89 92 3 493.18 1.22 254 89 139 50 205.81 5.09 255 92 140 48 205.83 5.09 256 93 97 4 473.91 3.97 257 93 98 5 471.55 5.14 258 93 140 47 205.93 5.12 259 94 97 3 494.16 0.35 260 95 98 3 493.96 2.75 261 95 137 42 206.30 5.04 262 95 140 45 206.19 5.02 263 96 99 3 493.95 1.89 264 96 100 4 478.19 1.82 265 97 100 3 479.24 4.57 266 97 101 4 471.59 0.77 267 98 101 3 481.37 1.56 268 98 102 4 462.09 3.95 269 98 133 35 206.75 5.13 270 98 136 38 206.75 5.12 271 98 137 39 206.75 5.13 272 98 140 42 206.69 5.12 273 99 102 3 474.43 5.04 274 99 103 4 464.89 2.56 275 100 103 3 481.55 1.47 276 100 104 4 465.64 2.14 277 101 104 3 470.84 0.48 278 101 105 4 464.87 2.50 279 102 105 3 472.99 1.56 280 102 106 4 471.55 0.84 281 102 129 27 207.77 5.40 282 102 133 31 207.09 5.16 283 103 106 3 471.53 0.85 284 103 107 4 471.52 0.85 285 104 107 3 470.95 1.14 286 104 108 4 469.45 1.89 287 105 108 3 472.67 0.28 288 105 109 4 469.44 1.89 289 105 129 24 208.18 5.25 290 106 109 3 476.22 2.05 291 106 110 4 467.50 2.31 292 106 117 11 210.69 5.38 293 106 122 16 208.40 5.26 294 106 125 19 208.36 5.25 295 106 126 20 208.31 5.26 296 106 129 23 208.28 5.25 297 107 110 3 476.22 2.06 298 107 111 4 469.99 2.10 299 108 111 3 473.70 3.31 300 108 112 4 470.00 2.10 301 109 112 3 475.30 2.52 302 109 113 4 469.97 2.10 303 109 125 16 209.14 5.46 304 110 113 3 471.89 1.73 305 110 117 7 213.72 4.70 306 113 116 3 484.66 3.46 307 113 117 4 435.41 5.09 308 115 118 3 525.28 0.22 309 116 121 5 438.00 7.59 310 117 121 4 438.03 7.61 311 117 122 5 427.16 2.18 312 117 125 8 420.46 4.48 313 118 121 3 476.98 2.06 314 118 122 4 444.91 4.21 315 119 122 3 470.31 1.55 316 119 123 4 460.43 3.39 317 120 123 3 476.52 1.24 318 120 124 4 467.30 3.37 319 121 124 3 472.64 0.99 320 121 125 4 467.31 3.37 321 122 125 3 481.59 1.28 322 122 126 4 472.70 3.17 323 123 126 3 480.51 0.61 324 123 127 4 480.38 0.68 325 124 127 3 480.50 0.61 326 124 128 4 470.14 1.97 327 125 128 3 472.57 0.96 328 125 129 4 470.16 1.96 329 126 129 3 479.19 2.36 330 126 130 4 469.93 1.84 331 127 130 3 472.42 1.02 332 127 131 4 472.22 0.70 333 128 131 3 472.64 0.91 334 128 132 4 472.22 0.70 335 129 132 3 472.22 0.70 336 129 133 4 472.22 0.70 337 130 133 3 470.01 0.41 338 130 134 4 466.63 2.15 339 131 134 3 472.51 0.79 340 131 135 4 466.64 2.15 341 132 135 3 480.08 4.57 342 132 136 4 462.60 4.17 343 133 136 3 471.60 0.33 344 133 137 4 462.60 4.17 345 134 137 3 486.29 1.43 346 134 138 4 467.63 2.32 347 135 138 3 472.47 0.83 348 136 140 4 487.70 3.37 349 137 140 3 485.35 2.66