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 5 458.55 1.86 2 2 127 125 26.48 1.01 3 2 128 126 26.14 0.85 4 2 131 129 26.08 0.87 5 3 6 3 466.50 0.83 6 3 7 4 464.82 0.03 7 3 127 124 34.74 0.50 8 4 7 3 471.72 0.77 9 4 8 4 464.82 0.03 10 5 8 3 475.09 0.92 11 5 9 4 463.76 0.56 12 6 9 3 474.97 5.04 13 6 10 4 463.45 0.59 14 6 124 118 46.99 0.29 15 6 127 121 46.18 0.68 16 7 11 4 463.25 0.63 17 7 73 66 46.97 0.29 18 7 74 67 46.97 0.29 19 8 11 3 458.62 3.00 20 8 12 4 458.19 3.15 21 9 13 4 452.84 4.04 22 9 121 112 63.75 0.18 23 9 124 115 63.66 0.17 24 10 13 3 485.81 1.49 25 10 14 4 452.66 4.13 26 10 70 60 63.70 0.19 27 10 124 114 63.75 0.19 28 10 125 115 63.70 0.18 29 10 128 118 63.65 0.17 30 11 15 4 462.55 3.63 31 11 70 59 63.72 0.20 32 11 71 60 63.72 0.20 33 11 73 62 63.72 0.20 34 12 15 3 473.30 1.74 35 12 16 4 467.08 1.38 36 12 116 104 82.84 0.08 37 13 16 3 482.62 2.93 38 13 17 4 473.62 1.57 39 13 113 100 85.85 1.56 40 13 116 103 82.78 0.11 41 13 121 108 76.80 0.57 42 13 125 112 67.58 1.33 43 14 17 3 467.04 1.43 44 14 63 49 74.91 0.27 45 14 66 52 64.59 0.18 46 14 67 53 66.22 0.67 47 14 70 56 64.51 0.17 48 14 105 91 82.52 0.02 49 14 109 95 82.88 0.08 50 16 113 97 93.10 1.32 51 16 116 100 92.88 1.33 52 17 20 3 483.84 1.51 53 17 21 4 452.72 4.73 54 17 24 7 413.07 11.88 55 17 109 92 93.03 1.31 56 17 113 96 97.06 0.10 57 18 21 3 506.81 0.64 58 20 23 3 474.47 0.88 59 20 24 4 473.40 0.35 60 21 24 3 480.54 2.15 61 21 25 4 469.11 1.80 62 21 63 42 99.98 0.84 63 21 64 43 99.97 0.85 64 22 25 3 474.49 0.87 65 22 26 4 469.12 1.80 66 22 59 37 108.55 2.99 67 22 60 38 102.61 2.10 68 22 63 41 102.62 2.10 69 23 26 3 476.33 0.06 70 23 27 4 469.12 1.81 71 23 112 89 135.78 0.74 72 24 27 3 476.31 0.06 73 24 28 4 468.67 1.89 74 24 108 84 124.89 1.60 75 24 109 85 133.22 1.75 76 24 112 88 135.80 0.75 77 24 113 89 135.80 0.73 78 25 28 3 471.98 3.67 79 25 29 4 467.45 2.50 80 25 59 34 118.68 0.36 81 25 63 38 118.64 0.35 82 26 29 3 470.41 1.22 83 26 30 4 468.14 2.25 84 26 56 30 134.34 1.35 85 26 59 33 121.50 1.77 86 27 30 3 478.44 1.05 87 27 31 4 474.47 0.91 88 27 108 81 136.09 0.77 89 27 112 85 136.87 0.56 90 28 31 3 482.99 0.10 91 28 32 4 474.48 0.91 92 28 101 73 136.01 0.79 93 28 104 76 136.02 0.79 94 28 105 77 136.01 0.80 95 28 108 80 136.56 0.64 96 29 32 3 482.20 0.29 97 29 33 4 478.44 1.08 98 29 55 26 136.45 0.70 99 29 58 29 136.16 0.82 100 29 59 30 136.15 0.83 101 29 62 33 136.12 0.82 102 29 101 72 136.07 0.78 103 30 33 3 479.70 2.66 104 30 34 4 474.68 2.96 105 30 50 20 137.40 0.64 106 30 56 26 136.94 0.55 107 31 34 3 479.43 0.59 108 31 35 4 474.68 2.96 109 31 104 73 136.75 0.45 110 31 107 76 137.27 0.68 111 31 108 77 137.26 0.65 112 31 111 80 137.48 0.67 113 32 35 3 475.31 2.69 114 32 36 4 462.23 3.27 115 32 39 7 342.88 1.23 116 32 100 68 136.74 0.43 117 32 101 69 136.75 0.45 118 32 104 72 137.02 0.56 119 33 37 4 438.62 0.66 120 33 39 6 310.63 3.86 121 33 40 7 298.29 2.76 122 33 43 10 221.09 35.82 123 33 48 15 137.50 0.65 124 33 55 22 137.45 0.66 125 34 37 3 474.94 1.59 126 36 39 3 489.87 1.09 127 36 100 64 136.94 0.53 128 36 103 67 137.53 0.68 129 36 104 68 137.53 0.68 130 37 40 3 482.73 1.01 131 38 41 3 485.60 0.42 132 39 42 3 487.24 0.40 133 39 43 4 487.24 0.40 134 39 97 58 136.91 0.55 135 39 100 61 137.53 0.70 136 40 43 3 487.24 0.40 137 40 48 8 137.91 0.66 138 42 93 51 136.72 0.47 139 42 94 52 137.41 0.68 140 42 97 55 137.55 0.69 141 43 46 3 478.56 1.74 142 43 48 5 420.69 11.87 143 43 58 15 147.50 3.85 144 45 54 9 148.75 3.72 145 46 54 8 148.74 3.72 146 46 55 9 148.75 3.72 147 46 58 12 148.71 3.73 148 47 52 5 314.04 11.25 149 47 54 7 148.77 3.72 150 47 55 8 148.76 3.72 151 48 55 7 148.78 3.71 152 49 52 3 473.69 2.62 153 51 56 5 448.47 2.90 154 52 55 3 475.95 2.58 155 52 56 4 455.34 0.51 156 53 56 3 464.94 1.62 157 53 57 4 459.02 1.32 158 54 57 3 467.00 2.67 159 54 58 4 459.04 1.33 160 55 58 3 471.84 4.53 161 55 59 4 471.84 4.53 162 56 60 4 477.28 1.79 163 57 60 3 485.42 1.81 164 57 61 4 484.95 2.04 165 58 61 3 484.95 2.04 166 58 62 4 470.20 3.07 167 59 62 3 472.62 4.28 168 59 63 4 470.20 3.07 169 60 63 3 472.24 2.06 170 60 64 4 464.34 4.16 171 61 64 3 483.19 0.97 172 61 65 4 469.82 1.45 173 62 65 3 483.98 0.58 174 62 66 4 481.07 0.07 175 62 101 39 183.06 3.79 176 63 66 3 481.88 0.48 177 63 67 4 481.09 0.07 178 64 67 3 481.07 0.07 179 64 68 4 481.07 0.07 180 65 68 3 485.99 1.01 181 65 69 4 476.02 2.60 182 65 83 18 171.12 1.39 183 66 69 3 478.64 0.62 184 66 70 4 473.94 1.73 185 66 105 39 207.80 0.09 186 66 129 63 199.72 2.71 187 66 132 66 187.17 5.86 188 67 70 3 473.94 1.72 189 67 71 4 466.81 1.84 190 68 71 3 466.56 1.97 191 68 72 4 466.56 1.97 192 68 80 12 188.94 6.62 193 69 73 4 447.23 1.43 194 69 76 7 282.80 3.26 195 69 80 11 183.51 4.01 196 69 128 59 218.75 4.92 197 69 132 63 205.82 1.42 198 70 73 3 471.52 0.09 199 70 128 58 230.43 0.74 200 72 75 3 482.47 1.18 201 72 76 4 466.06 2.29 202 72 79 7 319.50 8.09 203 73 76 3 472.53 0.15 204 73 128 55 255.71 1.81 205 75 78 3 489.23 0.85 206 75 79 4 451.12 1.24 207 76 79 3 474.98 5.53 208 76 80 4 451.50 1.42 209 76 128 52 262.38 3.76 210 76 131 55 261.92 3.68 211 76 132 56 261.50 3.50 212 76 135 59 256.63 2.08 213 77 81 4 455.09 3.22 214 77 135 58 258.13 2.81 215 77 140 63 238.50 1.67 216 78 81 3 467.48 1.77 217 80 83 3 470.56 2.71 218 80 84 4 465.50 0.18 219 80 132 52 265.66 2.44 220 80 135 55 262.74 3.83 221 80 136 56 262.72 3.83 222 80 140 60 261.42 3.64 223 81 84 3 471.06 2.46 224 81 85 4 465.54 0.21 225 81 140 59 261.25 3.72 226 82 85 3 471.97 2.96 227 82 86 4 466.01 0.03 228 83 86 3 471.98 2.96 229 83 87 4 466.01 0.02 230 83 136 53 266.83 2.25 231 84 87 3 469.40 1.72 232 84 88 4 461.15 2.39 233 84 89 5 461.12 2.40 234 84 135 51 266.83 2.23 235 84 136 52 266.82 2.23 236 84 138 54 266.81 2.24 237 84 140 56 266.75 2.25 238 84 141 57 266.66 2.29 239 85 89 4 418.32 16.68 240 85 90 5 411.07 20.30 241 85 141 56 266.58 2.33 242 86 90 4 411.06 20.30 243 86 91 5 411.06 20.30 244 87 91 4 376.61 7.88 245 87 92 5 354.94 18.69 246 87 93 6 354.90 18.68 247 87 98 11 301.66 7.25 248 87 136 49 266.88 2.23 249 88 92 4 367.65 12.34 250 88 136 48 266.88 2.23 251 88 137 49 266.84 2.25 252 88 138 50 266.83 2.25 253 88 139 51 266.82 2.25 254 88 141 53 266.82 2.25 255 89 92 3 484.19 1.55 256 89 139 50 266.80 2.25 257 89 141 52 266.80 2.25 258 93 97 4 482.12 0.29 259 93 98 5 469.50 6.03 260 94 97 3 485.90 0.93 261 95 98 3 478.66 1.46 262 95 99 4 478.67 1.45 263 95 137 42 267.39 2.19 264 96 99 3 478.67 1.45 265 96 100 4 478.67 1.45 266 97 100 3 484.88 4.57 267 97 101 4 474.49 3.52 268 98 101 3 489.73 2.14 269 98 102 4 463.95 1.38 270 98 133 35 267.49 2.19 271 98 136 38 267.54 2.18 272 98 137 39 267.49 2.19 273 99 102 3 475.25 0.90 274 99 103 4 470.88 2.10 275 100 103 3 477.10 1.81 276 100 104 4 474.29 0.41 277 101 104 3 474.29 0.41 278 101 105 4 474.28 0.41 279 102 105 3 472.98 2.33 280 102 106 4 473.98 3.23 281 102 129 27 267.99 2.23 282 102 133 31 267.97 2.23 283 103 106 3 474.38 3.02 284 103 107 4 473.98 3.23 285 104 107 3 481.12 0.34 286 104 108 4 473.98 3.23 287 105 108 3 481.12 0.34 288 105 109 4 474.12 3.15 289 105 129 24 268.77 2.00 290 106 109 3 475.19 0.82 291 106 110 4 469.78 0.97 292 106 117 11 270.20 1.76 293 106 122 16 269.11 2.02 294 106 125 19 268.92 1.95 295 106 126 20 268.88 1.97 296 106 129 23 268.88 1.96 297 107 110 3 472.01 2.08 298 107 111 4 472.62 0.46 299 108 111 3 479.93 0.61 300 108 112 4 469.77 0.96 301 109 112 3 468.60 2.46 302 109 113 4 449.49 8.78 303 109 125 16 269.12 1.97 304 110 114 4 441.37 12.83 305 110 117 7 273.42 0.32 306 111 114 3 495.61 2.10 307 113 116 3 483.56 1.53 308 113 117 4 479.83 0.34 309 114 117 3 483.56 1.53 310 115 118 3 515.90 0.98 311 116 121 5 453.86 10.85 312 117 122 5 435.84 5.98 313 117 125 8 421.43 2.81 314 118 121 3 475.17 0.20 315 118 122 4 470.17 1.41 316 119 122 3 478.45 1.84 317 119 123 4 470.18 1.41 318 120 123 3 485.11 6.06 319 120 124 4 470.17 1.41 320 121 124 3 477.55 2.27 321 121 125 4 468.90 2.04 322 122 125 3 479.68 2.04 323 122 126 4 456.71 4.53 324 123 126 3 473.80 0.40 325 123 127 4 457.47 6.00 326 124 127 3 470.78 1.91 327 124 128 4 457.47 6.00 328 125 128 3 482.03 1.12 329 125 129 4 458.04 5.71 330 126 129 3 474.19 2.04 331 126 130 4 462.45 7.91 332 127 130 3 472.91 1.40 333 127 131 4 463.45 6.12 334 128 131 3 475.14 0.47 335 128 132 4 468.25 3.72 336 129 132 3 468.24 3.71 337 129 133 4 468.43 3.62 338 130 133 3 471.57 1.41 339 130 134 4 469.55 0.21 340 131 134 3 480.38 2.00 341 131 135 4 474.84 0.76 342 132 135 3 486.30 4.04 343 132 136 4 474.10 0.37 344 133 136 3 481.19 1.50 345 133 137 4 475.19 0.59 346 134 137 3 480.71 1.74 347 134 138 4 474.43 0.21 348 135 138 3 485.56 3.75 349 135 140 5 454.31 10.26