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 5 448.82 1.46 2 2 73 71 30.71 0.66 3 2 76 74 26.20 0.58 4 2 127 125 22.82 0.09 5 2 128 126 22.47 0.24 6 3 6 3 476.09 0.58 7 3 7 4 467.81 4.73 8 4 7 3 475.74 0.76 9 4 8 4 467.80 4.73 10 5 8 3 478.70 0.71 11 5 9 4 459.74 0.64 12 6 9 3 469.58 5.28 13 6 10 4 453.37 0.68 14 6 124 118 45.61 0.01 15 6 127 121 45.20 0.19 16 7 10 3 478.57 0.78 17 7 11 4 459.66 2.64 18 7 73 66 46.07 0.38 19 7 74 67 49.12 1.14 20 8 11 3 473.89 0.57 21 8 12 4 470.88 2.05 22 9 12 3 478.80 0.98 23 9 13 4 470.88 2.05 24 9 121 112 59.23 0.45 25 9 124 115 59.20 0.47 26 10 13 3 480.62 1.90 27 10 14 4 462.29 6.32 28 10 70 60 59.40 0.35 29 10 124 114 59.36 0.39 30 10 125 115 59.23 0.45 31 10 128 118 59.22 0.45 32 11 14 3 479.70 2.35 33 11 15 4 462.06 6.45 34 11 70 59 59.35 0.32 35 11 73 62 59.41 0.35 36 12 15 3 475.03 2.81 37 12 16 4 471.29 0.94 38 13 16 3 479.57 0.54 39 13 17 4 467.14 1.14 40 13 121 108 59.92 0.21 41 13 125 112 59.87 0.23 42 14 17 3 468.73 1.95 43 14 18 4 463.31 4.66 44 14 21 7 407.03 4.61 45 14 66 52 59.89 0.21 46 14 67 53 59.89 0.20 47 14 70 56 59.87 0.21 48 14 109 95 67.59 2.87 49 15 18 3 472.00 0.32 50 16 116 100 76.34 1.33 51 17 20 3 486.70 0.20 52 17 21 4 461.11 5.75 53 17 24 7 407.80 0.03 54 17 109 92 75.78 1.05 55 17 113 96 86.77 2.97 56 18 21 3 494.95 4.26 57 20 23 3 471.87 1.52 58 20 24 4 468.64 1.94 59 21 24 3 468.75 2.00 60 21 25 4 466.00 3.38 61 21 63 42 87.23 2.94 62 22 25 3 470.78 0.98 63 22 26 4 465.99 3.37 64 22 60 38 88.65 3.62 65 22 63 41 88.64 3.62 66 23 26 3 473.56 0.41 67 23 27 4 462.50 5.11 68 24 27 3 482.00 4.63 69 24 28 4 464.42 0.73 70 24 108 84 119.41 1.24 71 24 109 85 120.21 0.43 72 24 112 88 126.53 2.04 73 25 28 3 469.12 1.52 74 25 29 4 464.54 0.78 75 25 59 34 116.59 0.10 76 26 29 3 468.14 0.34 77 26 30 4 464.55 0.78 78 26 55 29 126.17 1.33 79 26 56 30 123.48 2.64 80 26 59 33 117.53 0.36 81 27 30 3 467.42 1.91 82 27 31 4 465.30 1.16 83 27 108 81 127.95 1.79 84 27 112 85 128.49 1.73 85 28 31 3 470.15 3.37 86 28 32 4 465.31 1.16 87 28 101 73 127.64 1.83 88 28 104 76 127.67 1.83 89 28 105 77 127.64 1.81 90 28 108 80 128.10 1.73 91 29 32 3 467.42 2.94 92 29 33 4 464.57 1.52 93 29 55 26 128.31 1.71 94 29 58 29 128.21 1.75 95 29 59 30 128.12 1.72 96 29 101 72 127.70 1.84 97 30 33 3 479.92 2.91 98 30 34 4 464.57 1.53 99 30 50 20 128.69 1.61 100 31 34 3 473.43 0.07 101 31 35 4 464.54 1.51 102 31 104 73 127.83 1.86 103 31 107 76 128.54 1.69 104 31 108 77 128.47 1.65 105 32 35 3 476.10 0.40 106 32 36 4 453.55 2.69 107 32 39 7 321.76 10.45 108 32 101 69 127.73 1.86 109 32 104 72 128.25 1.67 110 33 37 4 444.69 1.65 111 33 39 6 344.18 14.46 112 33 40 7 288.29 11.68 113 33 43 10 196.44 24.68 114 33 48 15 128.91 1.65 115 33 55 22 128.81 1.61 116 34 37 3 479.35 0.87 117 36 39 3 493.45 4.57 118 36 100 64 127.75 1.85 119 36 103 67 128.79 1.57 120 36 104 68 128.79 1.58 121 37 40 3 480.70 0.27 122 38 41 3 482.36 0.45 123 39 42 3 485.91 0.90 124 39 97 58 127.70 1.84 125 39 100 61 128.79 1.56 126 40 43 3 476.86 0.35 127 40 48 8 129.34 1.70 128 41 44 3 496.12 2.64 129 42 93 51 127.33 1.80 130 42 94 52 128.40 1.59 131 42 97 55 128.80 1.56 132 43 46 3 476.62 3.40 133 43 48 5 380.75 29.64 134 43 58 15 129.57 1.42 135 45 54 9 189.43 30.66 136 46 54 8 189.38 30.66 137 46 58 12 189.34 30.65 138 47 52 5 211.62 19.59 139 47 54 7 191.40 29.70 140 47 55 8 191.40 29.70 141 48 52 4 398.91 7.15 142 48 55 7 194.15 29.60 143 49 52 3 476.68 0.52 144 52 55 3 478.81 1.93 145 52 56 4 467.57 3.91 146 53 56 3 472.01 1.70 147 53 57 4 446.98 2.93 148 54 57 3 465.66 4.86 149 54 58 4 465.78 3.64 150 55 58 3 474.22 0.57 151 55 59 4 465.79 3.65 152 56 59 3 473.55 0.24 153 56 60 4 474.28 0.60 154 57 60 3 480.66 2.58 155 57 61 4 474.28 0.60 156 58 61 3 474.25 0.60 157 58 62 4 474.28 0.62 158 59 62 3 476.60 0.54 159 59 63 4 473.50 1.01 160 60 63 3 473.63 0.95 161 60 64 4 473.62 0.95 162 61 64 3 480.69 2.58 163 61 65 4 473.62 0.95 164 62 65 3 480.05 1.96 165 62 66 4 466.85 4.63 166 63 66 3 468.97 3.58 167 63 67 4 463.03 4.34 168 64 67 3 466.85 2.43 169 64 68 4 459.75 4.16 170 65 68 3 468.16 0.04 171 65 69 4 466.74 0.69 172 65 80 15 155.24 1.46 173 65 83 18 155.13 1.41 174 66 69 3 477.01 4.44 175 66 70 4 466.77 0.68 176 66 105 39 181.90 3.21 177 66 128 62 187.77 0.62 178 66 129 63 172.19 1.64 179 66 132 66 159.49 0.48 180 67 70 3 477.08 0.46 181 67 71 4 472.17 2.02 182 68 71 3 477.10 0.45 183 68 72 4 472.17 2.02 184 68 79 11 163.50 2.73 185 69 72 3 477.17 0.48 186 69 73 4 472.06 2.06 187 69 76 7 315.56 25.26 188 69 80 11 163.00 2.47 189 69 128 59 187.87 0.62 190 69 132 63 172.12 1.57 191 70 73 3 472.06 2.06 192 70 128 58 190.52 1.95 193 72 75 3 470.57 0.71 194 72 76 4 429.91 7.64 195 72 79 7 279.44 1.89 196 73 76 3 481.21 2.39 197 73 128 55 242.61 7.28 198 75 78 3 475.99 0.60 199 75 79 4 449.75 5.40 200 76 79 3 471.71 1.49 201 76 80 4 432.34 11.60 202 76 128 52 254.87 12.04 203 76 131 55 251.99 11.08 204 76 132 56 244.94 7.67 205 77 81 4 432.84 9.55 206 77 135 58 244.15 8.05 207 78 81 3 470.92 0.55 208 80 83 3 481.92 1.08 209 80 84 4 473.88 5.77 210 80 132 52 254.91 12.02 211 80 135 55 254.53 12.12 212 80 136 56 254.50 12.12 213 81 84 3 480.63 2.40 214 81 85 4 473.88 5.77 215 81 139 58 254.53 12.13 216 82 85 3 481.87 1.79 217 82 86 4 473.89 5.76 218 83 86 3 475.97 4.72 219 83 87 4 473.86 5.76 220 83 136 53 254.84 12.03 221 84 87 3 479.13 2.93 222 84 88 4 461.39 2.56 223 84 135 51 254.88 12.03 224 84 136 52 254.81 12.04 225 84 138 54 254.80 12.03 226 84 139 55 254.77 12.04 227 85 88 3 478.00 3.49 228 85 89 4 457.47 4.53 229 85 139 54 254.74 12.06 230 86 89 3 485.26 0.14 231 86 90 4 447.22 4.82 232 86 91 5 447.21 4.82 233 87 91 4 409.78 8.04 234 87 92 5 409.71 8.01 235 87 98 11 280.75 8.96 236 87 136 49 254.96 12.01 237 87 140 53 254.78 12.04 238 88 92 4 397.33 14.20 239 88 139 51 254.83 12.04 240 88 140 52 254.66 12.04 241 89 92 3 491.81 2.61 242 92 140 48 254.96 12.00 243 93 97 4 482.00 1.77 244 93 98 5 473.50 3.12 245 93 140 47 255.01 12.02 246 94 97 3 486.62 0.01 247 95 98 3 482.70 1.42 248 95 140 45 255.24 11.98 249 96 99 3 485.80 2.96 250 96 100 4 481.40 2.04 251 97 100 3 481.98 1.76 252 97 101 4 476.53 4.48 253 98 101 3 479.48 1.54 254 98 102 4 471.94 2.19 255 98 133 35 255.70 11.90 256 98 136 38 255.72 11.92 257 98 140 42 255.69 11.91 258 99 102 3 470.98 1.56 259 99 103 4 466.02 0.77 260 100 103 3 475.04 0.48 261 100 104 4 469.93 1.21 262 101 104 3 470.88 1.60 263 101 105 4 465.44 0.47 264 102 105 3 473.47 2.89 265 102 106 4 467.14 0.40 266 102 129 27 256.25 11.90 267 102 133 31 256.25 11.89 268 103 106 3 473.69 0.04 269 103 107 4 467.14 0.41 270 104 107 3 470.22 1.96 271 104 108 4 466.18 0.07 272 105 108 3 466.18 0.06 273 105 109 4 466.17 0.07 274 105 129 24 256.94 12.00 275 106 109 3 472.23 2.42 276 106 110 4 468.19 0.42 277 106 117 11 258.48 11.67 278 106 122 16 257.54 11.88 279 106 125 19 257.41 11.93 280 106 126 20 257.39 11.93 281 106 129 23 257.25 11.86 282 107 110 3 473.87 3.25 283 107 111 4 463.75 1.81 284 108 111 3 476.56 2.69 285 108 112 4 465.63 2.77 286 109 112 3 471.78 5.85 287 109 113 4 448.88 3.96 288 109 125 16 257.94 11.76 289 110 113 3 481.56 0.96 290 110 117 7 259.61 11.34 291 113 116 3 479.60 0.32 292 113 117 4 462.19 2.78 293 114 117 3 483.32 1.54 294 115 118 3 522.32 1.08 295 116 121 5 459.24 0.37 296 117 121 4 462.10 0.28 297 117 122 5 459.00 0.48 298 117 125 8 427.06 0.96 299 118 121 3 470.00 0.60 300 118 122 4 462.12 0.28 301 119 122 3 476.16 3.69 302 119 123 4 462.12 0.28 303 120 123 3 479.15 2.19 304 120 124 4 465.26 1.29 305 121 124 3 465.73 1.06 306 121 125 4 464.35 0.81 307 122 125 3 476.05 2.79 308 122 126 4 473.79 3.93 309 123 126 3 475.86 2.90 310 123 127 4 473.81 3.92 311 124 127 3 467.94 0.98 312 124 128 4 464.35 0.81 313 125 128 3 469.68 1.90 314 125 129 4 469.63 0.14 315 126 129 3 480.31 2.77 316 126 130 4 465.78 1.79 317 127 130 3 476.88 3.14 318 127 131 4 464.01 0.91 319 128 131 3 478.23 3.81 320 128 132 4 465.74 1.17 321 129 132 3 477.62 2.76 322 129 133 4 464.05 0.85 323 130 133 3 468.41 0.46 324 130 134 4 464.18 0.78 325 131 134 3 467.22 1.27 326 131 135 4 466.42 0.58 327 132 135 3 469.08 0.99 328 132 136 4 466.23 0.48 329 133 136 3 478.19 3.23 330 133 137 4 463.06 1.11 331 134 137 3 469.00 1.86 332 134 138 4 461.69 0.42 333 135 138 3 478.17 2.93 334 136 140 4 491.57 0.32 335 137 140 3 479.29 2.14