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 5 455.36 4.54 2 2 73 71 31.80 0.17 3 2 76 74 28.73 1.10 4 2 127 125 21.81 0.36 5 2 128 126 21.61 0.19 6 3 6 3 475.94 0.52 7 3 7 4 469.12 2.31 8 4 7 3 474.47 0.33 9 4 8 4 474.44 0.32 10 5 8 3 477.06 1.54 11 5 9 4 474.44 0.34 12 6 9 3 477.72 1.21 13 6 10 4 474.45 0.34 14 6 124 118 47.18 0.79 15 6 127 121 47.18 0.79 16 7 10 3 477.05 1.54 17 7 11 4 474.44 0.34 18 7 73 66 48.43 0.76 19 7 74 67 50.73 0.34 20 8 11 3 476.19 0.54 21 8 12 4 469.22 2.94 22 9 12 3 477.05 0.10 23 9 13 4 469.16 2.92 24 9 121 112 59.90 0.58 25 9 124 115 59.85 0.58 26 10 13 3 478.88 1.02 27 10 14 4 469.12 2.91 28 10 70 60 60.23 0.76 29 10 124 114 59.91 0.58 30 10 125 115 59.87 0.58 31 10 128 118 59.85 0.57 32 11 14 3 477.05 1.93 33 11 15 4 455.38 4.83 34 11 70 59 60.23 0.76 35 11 71 60 60.37 0.81 36 11 73 62 60.34 0.82 37 12 15 3 474.41 0.61 38 12 16 4 469.56 1.80 39 13 16 3 477.82 1.42 40 13 17 4 465.45 0.24 41 13 121 108 60.76 0.82 42 13 125 112 60.73 0.80 43 14 17 3 465.04 0.46 44 14 18 4 465.03 0.46 45 14 21 7 409.47 1.72 46 14 63 49 72.61 2.35 47 14 66 52 60.75 0.80 48 14 67 53 60.77 0.82 49 14 70 56 60.74 0.80 50 14 109 95 72.98 2.36 51 15 18 3 466.61 1.24 52 16 113 97 95.58 1.55 53 16 116 100 93.89 0.72 54 17 20 3 484.95 0.68 55 17 21 4 437.32 8.03 56 17 24 7 401.61 5.07 57 17 109 92 93.85 0.74 58 17 113 96 95.72 1.60 59 18 21 3 493.20 3.39 60 20 23 3 473.49 1.04 61 20 24 4 469.04 0.10 62 21 24 3 468.12 0.57 63 21 25 4 467.06 1.09 64 21 63 42 98.12 1.45 65 22 25 3 473.39 0.50 66 22 26 4 471.81 1.28 67 22 60 38 98.34 1.51 68 22 63 41 98.33 1.51 69 23 26 3 481.83 4.72 70 23 27 4 469.62 2.38 71 23 56 33 118.61 0.15 72 24 27 3 482.82 4.22 73 24 28 4 468.66 2.86 74 24 108 84 118.67 0.14 75 24 109 85 120.60 0.28 76 24 112 88 127.48 0.72 77 25 28 3 473.26 0.56 78 25 29 4 469.00 2.69 79 25 59 34 118.60 0.14 80 25 63 38 118.24 0.01 81 25 105 80 118.68 0.14 82 26 29 3 470.66 1.86 83 26 30 4 466.48 0.23 84 26 55 29 126.87 0.90 85 26 56 30 125.47 1.53 86 26 59 33 118.45 0.10 87 27 30 3 465.64 0.66 88 27 31 4 463.62 0.36 89 27 108 81 128.13 0.45 90 27 112 85 129.26 0.04 91 28 31 3 470.17 1.61 92 28 32 4 458.32 2.29 93 28 101 73 127.64 0.65 94 28 104 76 127.66 0.65 95 28 105 77 127.66 0.64 96 28 108 80 128.15 0.45 97 29 32 3 471.06 1.16 98 29 33 4 465.67 2.06 99 29 55 26 128.58 0.24 100 29 58 29 128.56 0.27 101 29 59 30 127.74 0.66 102 29 101 72 127.70 0.65 103 30 33 3 485.40 0.53 104 30 34 4 464.64 1.55 105 30 50 20 129.42 0.07 106 31 34 3 482.74 1.86 107 31 35 4 457.79 1.87 108 31 104 73 128.85 0.12 109 31 107 76 128.94 0.10 110 31 108 77 128.94 0.11 111 31 111 80 129.47 0.07 112 32 35 3 473.34 0.02 113 32 36 4 456.49 1.23 114 32 39 7 310.77 0.82 115 32 101 69 128.84 0.12 116 32 104 72 128.89 0.11 117 33 37 4 426.39 7.48 118 33 39 6 345.98 18.42 119 33 40 7 329.37 26.73 120 33 43 10 220.21 28.71 121 33 48 15 129.56 0.07 122 34 37 3 482.88 0.90 123 36 39 3 491.28 5.66 124 36 100 64 128.89 0.14 125 36 103 67 129.38 0.06 126 36 104 68 129.38 0.06 127 37 40 3 480.01 0.08 128 38 41 3 487.93 1.44 129 39 42 3 484.31 0.10 130 39 43 4 481.98 1.10 131 39 97 58 128.88 0.12 132 39 100 61 129.28 0.03 133 40 43 3 494.28 1.80 134 40 48 8 134.67 1.22 135 41 44 3 494.29 1.80 136 42 93 51 128.77 0.12 137 42 94 52 128.96 0.09 138 42 97 55 129.27 0.04 139 43 46 3 477.87 1.02 140 43 48 5 405.85 2.22 141 43 58 15 132.35 1.34 142 45 54 9 135.49 0.26 143 46 54 8 135.48 0.26 144 46 58 12 135.47 0.26 145 47 52 5 211.53 33.12 146 47 54 7 135.50 0.26 147 47 55 8 135.51 0.26 148 48 52 4 412.45 5.50 149 48 55 7 152.49 8.23 150 49 52 3 475.97 0.88 151 52 55 3 470.41 2.65 152 52 56 4 465.86 4.79 153 53 56 3 465.86 4.79 154 53 57 4 472.51 1.47 155 54 57 3 472.51 1.47 156 54 58 4 472.53 1.48 157 55 58 3 476.35 3.39 158 55 59 4 472.53 1.48 159 56 59 3 474.35 1.68 160 56 60 4 472.53 1.48 161 57 60 3 483.92 4.21 162 57 61 4 472.53 1.48 163 58 61 3 472.73 1.36 164 58 62 4 471.06 0.76 165 59 62 3 474.84 0.34 166 59 63 4 465.67 1.36 167 60 63 3 472.52 1.50 168 60 64 4 471.95 1.79 169 61 64 3 472.53 1.50 170 61 65 4 471.88 1.82 171 62 65 3 478.59 2.69 172 62 66 4 474.07 0.72 173 63 66 3 475.68 1.52 174 63 67 4 471.87 1.83 175 64 67 3 468.01 2.31 176 64 68 4 462.69 0.35 177 65 68 3 472.89 4.75 178 65 69 4 464.07 0.34 179 65 80 15 154.34 1.80 180 65 83 18 152.12 0.78 181 66 69 3 478.96 1.71 182 66 70 4 462.68 0.35 183 66 105 39 167.78 1.79 184 66 128 62 168.75 1.67 185 66 129 63 158.31 0.07 186 66 132 66 154.77 1.71 187 67 70 3 469.97 4.00 188 67 71 4 468.01 2.33 189 68 71 3 475.07 1.19 190 68 72 4 467.99 2.35 191 68 79 11 212.58 20.68 192 69 72 3 475.41 1.36 193 69 73 4 451.13 1.17 194 69 76 7 290.97 5.18 195 69 80 11 156.08 1.11 196 69 128 59 172.03 0.05 197 69 132 63 171.47 0.13 198 70 73 3 470.31 1.19 199 70 128 58 180.50 4.26 200 72 75 3 471.42 0.29 201 72 76 4 442.43 14.20 202 72 79 7 281.55 1.46 203 73 76 3 477.25 2.62 204 75 78 3 483.22 0.32 205 75 79 4 459.72 3.35 206 76 79 3 468.80 1.18 207 76 80 4 440.44 3.29 208 76 128 52 260.34 4.67 209 76 131 55 259.04 4.04 210 76 132 56 258.25 3.87 211 77 81 4 440.44 3.29 212 77 135 58 251.96 6.98 213 78 81 3 469.18 1.42 214 80 83 3 479.44 0.58 215 80 84 4 472.23 4.85 216 80 132 52 262.29 5.48 217 80 135 55 262.28 5.50 218 80 136 56 262.32 5.51 219 81 84 3 478.88 1.53 220 81 85 4 472.23 4.85 221 81 139 58 262.34 5.50 222 82 85 3 480.11 0.91 223 82 86 4 483.47 0.77 224 83 86 3 483.47 0.78 225 83 87 4 483.47 0.77 226 83 136 53 262.88 5.70 227 84 87 3 483.47 0.78 228 84 88 4 468.95 8.02 229 84 135 51 262.99 5.71 230 84 136 52 262.87 5.70 231 84 138 54 262.91 5.71 232 84 139 55 262.85 5.73 233 85 88 3 478.64 3.19 234 85 89 4 468.94 8.02 235 85 139 54 262.88 5.71 236 86 89 3 485.32 0.17 237 86 90 4 447.66 2.59 238 86 91 5 420.14 3.46 239 87 91 4 383.74 5.00 240 87 92 5 337.22 9.89 241 87 98 11 267.25 5.80 242 87 136 49 263.01 5.70 243 87 140 53 262.89 5.72 244 88 92 4 381.62 3.95 245 88 139 51 262.92 5.71 246 88 140 52 262.82 5.69 247 89 92 3 492.91 3.16 248 92 140 48 263.00 5.70 249 93 97 4 477.35 0.56 250 93 98 5 471.75 2.24 251 93 140 47 263.06 5.71 252 94 97 3 484.87 0.86 253 95 98 3 484.98 0.81 254 95 137 42 263.44 5.59 255 95 140 45 263.44 5.60 256 96 99 3 491.77 5.60 257 96 100 4 480.94 0.53 258 97 100 3 480.95 0.54 259 97 101 4 481.19 0.40 260 98 101 3 479.40 1.58 261 98 102 4 470.49 1.21 262 98 133 35 264.04 5.58 263 98 136 38 264.06 5.59 264 98 137 39 264.05 5.59 265 98 140 42 264.05 5.59 266 99 102 3 476.77 1.81 267 99 103 4 474.42 0.79 268 100 103 3 475.50 2.45 269 100 104 4 473.29 1.35 270 101 104 3 469.30 0.64 271 101 105 4 466.24 0.90 272 102 105 3 474.69 0.53 273 102 106 4 466.37 0.96 274 102 129 27 265.10 5.47 275 102 133 31 264.19 5.55 276 103 106 3 473.04 0.29 277 103 107 4 466.41 0.97 278 104 107 3 467.94 1.74 279 104 108 4 466.94 0.70 280 105 108 3 472.75 2.20 281 105 109 4 469.53 0.56 282 105 129 24 265.81 5.48 283 106 109 3 472.96 2.27 284 106 110 4 466.98 0.72 285 106 117 11 266.67 5.54 286 106 125 19 266.21 5.42 287 106 126 20 266.05 5.50 288 106 129 23 266.08 5.43 289 107 110 3 472.66 2.10 290 107 111 4 464.77 1.83 291 108 111 3 473.44 2.50 292 108 112 4 464.55 1.95 293 109 112 3 480.18 1.65 294 109 113 4 460.97 3.73 295 109 125 16 266.31 5.46 296 110 113 3 479.81 1.83 297 110 117 7 266.68 5.54 298 113 116 3 477.10 0.93 299 113 117 4 455.13 3.08 300 115 118 3 526.28 0.91 301 116 121 5 458.88 0.14 302 117 121 4 458.88 0.14 303 117 122 5 453.00 2.50 304 117 125 8 408.20 6.71 305 118 121 3 467.38 1.06 306 118 122 4 464.92 2.88 307 119 122 3 467.97 1.35 308 119 123 4 462.52 1.68 309 120 123 3 474.92 2.12 310 120 124 4 474.41 1.88 311 121 124 3 478.50 0.17 312 121 125 4 472.02 3.07 313 122 125 3 474.42 1.98 314 122 126 4 472.02 3.07 315 123 126 3 474.22 2.08 316 123 127 4 471.73 3.21 317 124 127 3 473.61 2.29 318 124 128 4 465.86 0.28 319 125 128 3 474.00 2.71 320 125 129 4 467.89 0.73 321 126 129 3 484.62 0.62 322 126 130 4 468.89 1.24 323 127 130 3 476.49 4.69 324 127 131 4 465.66 2.85 325 128 131 3 476.48 4.69 326 128 132 4 466.57 2.39 327 129 132 3 475.88 3.64 328 129 133 4 460.99 0.41 329 130 133 3 472.86 3.60 330 130 134 4 468.21 4.01 331 131 134 3 473.59 1.53 332 131 135 4 460.53 0.18 333 132 135 3 474.12 5.26 334 132 136 4 460.53 0.18 335 133 136 3 477.09 3.78 336 133 137 4 462.59 0.51 337 134 137 3 479.28 2.38 338 134 138 4 459.16 1.22 339 135 138 3 479.28 2.38 340 136 140 4 491.44 0.39 341 137 140 3 485.50 0.97