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 5 448.57 1.85 2 2 73 71 30.95 0.14 3 2 76 74 28.64 1.01 4 2 127 125 23.66 0.12 5 2 128 126 23.66 0.12 6 2 131 129 23.64 0.13 7 3 6 3 469.92 5.03 8 3 7 4 468.00 2.56 9 4 7 3 476.30 1.84 10 4 8 4 470.38 1.40 11 5 8 3 477.47 2.42 12 5 9 4 470.98 1.10 13 6 9 3 472.99 0.18 14 6 10 4 471.07 1.15 15 6 124 118 45.83 0.21 16 6 127 121 45.84 0.21 17 7 10 3 474.75 0.40 18 7 11 4 471.12 1.17 19 7 73 66 47.74 0.18 20 7 74 67 47.90 0.26 21 8 11 3 477.23 0.84 22 8 12 4 471.07 1.16 23 9 12 3 478.95 0.62 24 9 13 4 474.69 0.61 25 9 121 112 56.09 0.59 26 9 124 115 56.08 0.59 27 10 13 3 478.06 1.06 28 10 14 4 469.81 2.17 29 10 70 60 56.30 0.48 30 10 124 114 56.10 0.59 31 10 125 115 56.08 0.59 32 10 128 118 56.08 0.59 33 11 14 3 479.43 0.32 34 11 15 4 466.42 6.83 35 11 70 59 56.30 0.48 36 11 73 62 56.66 0.37 37 12 15 3 483.04 1.18 38 12 16 4 474.30 2.91 39 13 16 3 477.88 1.12 40 13 17 4 477.88 1.12 41 13 113 100 75.38 2.29 42 13 121 108 63.66 2.69 43 13 125 112 63.53 2.74 44 14 17 3 474.31 2.91 45 14 18 4 474.31 2.91 46 14 21 7 414.85 3.71 47 14 63 49 70.73 0.84 48 14 66 52 63.56 2.74 49 14 67 53 63.55 2.73 50 14 70 56 63.55 2.73 51 14 109 95 74.94 2.46 52 15 18 3 477.97 1.07 53 16 113 97 84.37 2.14 54 16 116 100 84.33 2.12 55 17 20 3 485.54 4.66 56 17 21 4 457.89 1.61 57 17 24 7 420.56 4.27 58 17 109 92 84.29 2.17 59 17 113 96 84.41 2.15 60 18 21 3 503.33 1.19 61 20 23 3 478.01 1.17 62 20 24 4 468.02 2.25 63 21 24 3 469.82 1.35 64 21 25 4 468.01 2.25 65 21 63 42 91.81 1.22 66 22 25 3 468.04 2.25 67 22 26 4 468.03 2.25 68 22 60 38 96.87 1.25 69 22 63 41 93.00 1.81 70 23 26 3 474.95 0.11 71 23 27 4 464.10 0.29 72 24 27 3 469.97 5.36 73 24 28 4 462.68 1.72 74 24 108 84 123.56 1.04 75 24 109 85 125.78 0.25 76 24 112 88 128.77 0.58 77 25 28 3 473.91 0.78 78 25 29 4 462.70 1.74 79 25 59 34 115.47 0.30 80 26 29 3 477.88 0.13 81 26 30 4 462.50 1.83 82 26 55 29 127.47 1.26 83 26 56 30 123.09 0.94 84 26 59 33 118.09 1.60 85 27 30 3 474.99 1.32 86 27 31 4 462.46 1.85 87 27 108 81 129.15 0.69 88 27 112 85 130.12 1.03 89 28 31 3 469.18 2.81 90 28 32 4 460.44 2.85 91 28 101 73 129.09 0.70 92 28 104 76 129.09 0.70 93 28 105 77 129.06 0.69 94 28 108 80 129.16 0.69 95 29 32 3 464.07 2.85 96 29 33 4 463.31 2.48 97 29 55 26 129.27 0.63 98 29 58 29 129.19 0.67 99 29 59 30 129.18 0.68 100 29 101 72 129.15 0.69 101 30 33 3 470.01 2.39 102 30 34 4 463.82 0.70 103 30 50 20 130.20 1.06 104 31 34 3 474.72 1.40 105 31 35 4 455.75 4.74 106 31 104 73 129.64 0.93 107 31 107 76 130.15 1.07 108 31 108 77 130.12 1.06 109 32 35 3 467.36 1.07 110 32 36 4 446.10 1.73 111 32 39 7 320.33 2.73 112 32 101 69 129.62 0.94 113 32 104 72 129.97 1.07 114 33 37 4 443.27 0.33 115 33 39 6 320.32 2.73 116 33 40 7 294.60 3.06 117 33 43 10 302.10 3.91 118 33 48 15 130.27 1.08 119 33 55 22 130.24 1.07 120 34 37 3 490.24 1.35 121 36 39 3 499.94 3.65 122 36 100 64 129.68 0.95 123 36 103 67 130.20 1.08 124 36 104 68 130.21 1.08 125 37 40 3 488.63 1.03 126 38 41 3 489.64 2.42 127 39 42 3 493.58 0.48 128 39 43 4 489.53 1.38 129 39 97 58 129.69 0.97 130 39 100 61 130.16 1.09 131 40 43 3 488.25 0.74 132 40 44 4 484.25 0.10 133 40 48 8 210.62 34.08 134 41 44 3 497.34 1.09 135 42 45 3 646.57 0.43 136 42 93 51 129.68 1.01 137 42 94 52 129.91 1.09 138 42 97 55 130.16 1.09 139 43 46 3 486.12 0.48 140 43 48 5 412.05 2.47 141 43 58 15 137.31 2.21 142 45 54 9 141.48 0.53 143 46 54 8 141.47 0.53 144 46 55 9 141.47 0.53 145 46 58 12 141.46 0.54 146 47 52 5 236.06 25.98 147 47 54 7 141.48 0.54 148 47 55 8 141.49 0.54 149 48 55 7 141.50 0.54 150 49 52 3 479.13 2.27 151 51 56 5 462.69 4.60 152 52 55 3 477.20 0.59 153 52 56 4 468.74 1.59 154 53 56 3 478.38 3.23 155 53 57 4 468.85 1.65 156 54 57 3 476.69 1.57 157 54 58 4 465.93 3.12 158 55 58 3 476.21 1.82 159 55 59 4 465.92 3.12 160 56 59 3 473.36 0.59 161 56 60 4 473.50 0.67 162 57 60 3 473.49 0.68 163 57 61 4 473.49 0.68 164 58 61 3 473.49 0.68 165 58 62 4 473.48 0.68 166 59 62 3 480.50 2.83 167 59 63 4 473.49 0.68 168 60 63 3 473.51 0.54 169 60 64 4 473.28 0.66 170 61 64 3 473.34 0.63 171 61 65 4 473.25 0.66 172 62 65 3 479.12 3.52 173 62 66 4 467.84 1.48 174 62 101 39 138.83 2.94 175 63 66 3 477.49 3.35 176 63 67 4 469.15 0.54 177 64 67 3 477.19 3.50 178 64 68 4 469.14 0.53 179 65 68 3 473.66 0.65 180 65 69 4 466.30 0.90 181 65 80 15 141.12 3.21 182 65 83 18 139.68 2.50 183 66 69 3 472.74 0.97 184 66 70 4 466.30 0.91 185 66 105 39 180.92 0.39 186 66 132 66 141.03 3.31 187 67 70 3 474.03 3.44 188 67 71 4 457.42 5.34 189 68 71 3 477.55 1.68 190 68 72 4 460.53 3.79 191 68 79 11 174.91 2.04 192 68 80 12 174.92 2.03 193 69 72 3 477.28 1.54 194 69 73 4 447.40 0.49 195 69 76 7 317.50 19.37 196 69 80 11 174.93 2.04 197 69 128 59 194.97 0.73 198 69 132 63 176.55 2.84 199 70 73 3 463.31 8.53 200 70 128 58 195.02 0.76 201 72 75 3 465.77 2.67 202 72 76 4 440.73 7.05 203 72 79 7 306.11 3.18 204 73 76 3 475.53 1.43 205 73 128 55 271.90 1.56 206 75 78 3 495.31 0.51 207 75 79 4 458.46 1.76 208 76 79 3 473.22 4.15 209 76 80 4 458.46 1.77 210 76 128 52 275.61 1.75 211 76 131 55 274.11 1.78 212 76 132 56 272.85 1.69 213 76 135 59 272.85 1.69 214 77 80 3 486.94 1.12 215 77 81 4 454.03 3.98 216 77 135 58 272.85 1.69 217 78 81 3 472.33 3.70 218 80 83 3 474.07 1.59 219 80 84 4 453.85 8.57 220 80 132 52 276.18 1.63 221 80 135 55 275.89 1.64 222 80 136 56 275.88 1.62 223 81 84 3 473.21 0.25 224 81 85 4 467.26 1.88 225 81 139 58 275.89 1.63 226 82 85 3 473.29 1.27 227 82 86 4 469.32 3.25 228 83 86 3 474.88 2.06 229 83 87 4 466.69 2.16 230 83 136 53 276.13 1.60 231 84 87 3 474.00 2.50 232 84 88 4 461.60 4.69 233 84 135 51 276.26 1.61 234 84 136 52 276.13 1.60 235 84 139 55 276.08 1.59 236 85 88 3 474.81 2.07 237 85 89 4 461.48 4.65 238 85 139 54 276.10 1.60 239 86 90 4 390.41 12.11 240 86 91 5 362.93 15.54 241 87 91 4 374.12 9.94 242 87 92 5 290.56 7.00 243 87 98 11 280.53 2.70 244 87 136 49 276.32 1.63 245 87 140 53 276.12 1.60 246 88 92 4 318.21 6.82 247 88 139 51 276.21 1.63 248 88 140 52 276.11 1.60 249 89 92 3 487.57 1.98 250 89 139 50 276.30 1.63 251 92 140 48 276.30 1.63 252 93 97 4 479.19 1.43 253 93 98 5 476.82 0.25 254 93 140 47 276.38 1.65 255 94 97 3 492.03 1.44 256 95 98 3 491.98 1.47 257 95 137 42 276.66 1.68 258 95 140 45 276.57 1.65 259 96 99 3 493.18 0.32 260 96 100 4 479.18 1.43 261 97 100 3 474.42 0.77 262 97 101 4 474.47 0.79 263 98 101 3 480.79 3.74 264 98 102 4 474.47 0.79 265 98 133 35 277.11 1.71 266 98 136 38 277.15 1.69 267 98 137 39 277.11 1.71 268 98 140 42 277.12 1.71 269 99 102 3 480.57 3.85 270 99 103 4 474.45 0.81 271 100 103 3 480.32 3.97 272 100 104 4 474.22 0.93 273 101 104 3 480.32 3.98 274 101 105 4 472.38 1.84 275 102 105 3 476.01 3.66 276 102 106 4 472.70 2.00 277 102 129 27 277.38 1.63 278 102 133 31 277.38 1.63 279 103 106 3 476.90 0.10 280 103 107 4 476.91 0.10 281 104 107 3 482.71 2.79 282 104 108 4 469.97 3.57 283 105 108 3 482.70 2.79 284 105 109 4 469.97 3.58 285 105 129 24 278.04 1.81 286 106 109 3 483.36 3.10 287 106 110 4 476.79 0.18 288 106 117 11 278.69 1.67 289 106 122 16 278.17 1.79 290 106 125 19 278.13 1.80 291 106 126 20 278.08 1.82 292 106 129 23 278.07 1.82 293 107 110 3 476.80 0.18 294 107 111 4 476.79 0.18 295 108 111 3 477.98 0.41 296 108 112 4 476.79 0.18 297 109 112 3 480.28 1.54 298 109 113 4 459.24 0.75 299 109 125 16 278.25 1.82 300 110 113 3 480.28 1.54 301 110 117 7 278.76 1.72 302 113 116 3 468.47 3.39 303 113 117 4 444.19 6.79 304 116 121 5 430.81 3.68 305 117 122 5 430.85 3.70 306 117 125 8 375.47 7.13 307 118 121 3 472.28 0.53 308 118 122 4 464.06 3.58 309 119 122 3 482.84 2.91 310 119 123 4 456.34 0.29 311 120 123 3 475.82 0.59 312 120 124 4 462.66 1.57 313 121 124 3 468.41 1.43 314 121 125 4 462.84 2.62 315 122 125 3 483.92 2.97 316 122 126 4 472.13 2.02 317 123 126 3 478.24 0.54 318 123 127 4 473.75 1.21 319 124 127 3 478.18 0.55 320 124 128 4 474.00 1.33 321 125 128 3 475.31 1.99 322 125 129 4 473.75 1.21 323 126 129 3 478.50 0.38 324 126 130 4 472.52 2.08 325 127 130 3 477.05 0.18 326 127 131 4 472.52 2.08 327 128 131 3 473.62 1.53 328 128 132 4 473.62 1.53 329 129 132 3 473.62 1.53 330 129 133 4 464.09 1.40 331 130 133 3 470.26 0.15 332 130 134 4 464.09 1.40 333 131 134 3 469.14 0.41 334 131 135 4 463.33 1.78 335 132 135 3 466.50 0.19 336 132 136 4 463.30 1.77 337 133 136 3 471.69 2.43 338 133 137 4 462.81 2.01 339 134 137 3 473.67 1.58 340 134 138 4 460.80 1.16 341 135 138 3 470.46 3.26 342 136 140 4 494.06 3.52 343 137 140 3 486.87 0.07