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 5 441.14 0.53 2 2 73 71 31.74 0.14 3 2 76 74 25.78 0.38 4 2 127 125 23.68 0.52 5 2 128 126 23.73 0.42 6 2 131 129 23.21 0.61 7 3 6 3 476.05 0.46 8 3 7 4 479.33 2.10 9 4 7 3 479.33 2.10 10 4 8 4 474.48 0.33 11 5 8 3 481.83 0.85 12 5 9 4 474.47 0.33 13 6 9 3 477.05 1.54 14 6 10 4 474.44 0.33 15 6 124 118 48.08 0.55 16 6 127 121 47.98 0.41 17 7 10 3 476.95 1.59 18 7 11 4 465.29 4.87 19 7 73 66 48.61 0.67 20 7 74 67 49.27 0.34 21 8 11 3 474.65 0.19 22 8 12 4 469.15 2.93 23 9 12 3 477.05 0.10 24 9 13 4 469.12 2.92 25 9 121 112 60.04 0.18 26 9 124 115 59.77 0.04 27 10 13 3 486.09 2.59 28 10 14 4 448.64 2.63 29 10 70 60 59.76 0.07 30 10 124 114 60.11 0.21 31 10 125 115 59.74 0.06 32 10 128 118 59.74 0.06 33 11 15 4 451.31 3.97 34 11 70 59 60.08 0.23 35 11 71 60 60.22 0.29 36 11 73 62 60.21 0.29 37 12 15 3 468.38 2.40 38 12 16 4 469.54 1.81 39 13 16 3 482.35 0.85 40 13 17 4 465.38 0.27 41 13 113 100 80.95 0.18 42 13 121 108 62.16 0.34 43 13 125 112 60.84 0.33 44 14 17 3 462.59 1.67 45 14 18 4 464.34 2.40 46 14 21 7 414.44 3.40 47 14 63 49 75.48 0.92 48 14 66 52 60.84 0.33 49 14 67 53 66.92 3.36 50 14 70 56 60.84 0.33 51 15 18 3 473.59 0.65 52 16 113 97 91.26 1.96 53 16 116 100 90.83 1.93 54 17 20 3 482.35 0.62 55 17 21 4 434.53 2.44 56 17 24 7 406.78 2.48 57 17 109 92 88.17 0.64 58 17 113 96 94.30 2.35 59 18 21 3 492.73 3.63 60 20 23 3 470.12 0.65 61 20 24 4 468.93 0.05 62 21 24 3 468.96 0.07 63 21 25 4 466.88 1.06 64 21 63 42 98.07 1.50 65 22 25 3 470.61 0.90 66 22 26 4 468.00 0.51 67 22 60 38 101.52 0.18 68 22 63 41 98.95 1.09 69 23 26 3 482.82 4.22 70 23 27 4 463.10 2.30 71 24 27 3 482.82 4.22 72 24 28 4 463.35 2.18 73 24 108 84 117.68 0.01 74 24 109 85 122.45 0.28 75 24 112 88 128.56 1.16 76 25 28 3 473.25 0.56 77 25 29 4 468.99 2.69 78 25 59 34 117.06 0.14 79 25 63 38 116.70 0.05 80 26 29 3 475.79 0.70 81 26 30 4 468.64 1.60 82 26 55 29 127.28 1.04 83 26 56 30 127.28 1.04 84 26 59 33 117.44 0.40 85 27 30 3 469.39 1.24 86 27 31 4 465.39 3.23 87 27 108 81 128.88 1.22 88 27 112 85 129.62 1.18 89 28 31 3 468.49 2.44 90 28 32 4 465.39 3.21 91 28 101 73 128.67 1.20 92 28 104 76 128.68 1.20 93 28 105 77 128.72 1.23 94 28 108 80 128.91 1.23 95 29 32 3 470.69 0.97 96 29 33 4 466.47 1.38 97 29 55 26 129.03 1.26 98 29 58 29 128.91 1.21 99 29 59 30 128.88 1.23 100 29 101 72 128.80 1.20 101 30 33 3 480.93 1.71 102 30 34 4 466.47 1.38 103 30 50 20 129.56 1.17 104 31 34 3 468.91 1.87 105 31 35 4 457.93 2.98 106 31 104 73 128.98 1.20 107 31 107 76 129.59 1.16 108 31 108 77 129.60 1.16 109 32 35 3 474.35 0.48 110 32 36 4 454.22 4.83 111 32 39 7 329.72 13.09 112 32 101 69 128.94 1.19 113 32 104 72 129.09 1.15 114 33 37 4 423.42 3.10 115 33 39 6 380.99 24.32 116 33 40 7 276.83 5.79 117 33 43 10 276.81 5.79 118 33 48 15 129.75 1.15 119 34 37 3 482.88 0.90 120 36 39 3 493.38 4.61 121 36 100 64 129.07 1.16 122 36 103 67 129.63 1.16 123 36 104 68 129.65 1.15 124 37 40 3 480.01 0.08 125 38 41 3 488.05 1.38 126 39 42 3 486.45 0.97 127 39 43 4 483.04 0.58 128 39 97 58 128.99 1.20 129 39 100 61 129.62 1.17 130 40 43 3 494.28 1.80 131 40 44 4 479.09 1.47 132 40 48 8 254.84 0.81 133 41 44 3 498.08 0.10 134 42 93 51 128.77 1.08 135 42 94 52 129.23 1.17 136 42 97 55 129.64 1.17 137 43 46 3 477.99 0.97 138 43 48 5 445.66 2.81 139 43 58 15 188.14 27.84 140 45 54 9 255.00 0.79 141 46 54 8 255.00 0.79 142 46 55 9 255.00 0.79 143 46 58 12 254.90 0.83 144 47 52 5 265.06 4.21 145 47 54 7 255.01 0.79 146 47 55 8 255.00 0.79 147 48 52 4 366.30 2.93 148 48 55 7 255.00 0.79 149 49 52 3 475.97 0.88 150 52 55 3 470.41 2.65 151 52 56 4 471.79 1.81 152 53 56 3 471.79 1.81 153 53 57 4 471.78 1.81 154 54 57 3 471.79 1.82 155 54 58 4 472.48 1.47 156 55 58 3 472.54 1.42 157 55 59 4 472.51 1.43 158 56 59 3 473.70 2.00 159 56 60 4 472.65 1.48 160 57 60 3 483.98 4.19 161 57 61 4 472.64 1.49 162 58 61 3 474.89 0.36 163 58 62 4 472.63 1.49 164 59 62 3 479.87 1.05 165 59 63 4 472.55 1.52 166 60 63 3 473.62 2.01 167 60 64 4 471.93 1.79 168 61 64 3 471.43 1.54 169 61 65 4 473.56 0.48 170 62 65 3 483.15 0.40 171 62 66 4 467.97 2.32 172 62 101 39 138.03 4.26 173 63 66 3 478.30 2.83 174 63 67 4 468.13 0.03 175 64 67 3 470.36 1.14 176 64 68 4 464.63 1.72 177 65 68 3 475.23 3.58 178 65 69 4 466.41 0.83 179 65 83 18 131.24 1.23 180 66 69 3 479.93 1.23 181 66 70 4 466.41 0.83 182 66 105 39 176.68 2.48 183 66 129 63 162.04 2.69 184 66 132 66 147.11 0.27 185 67 70 3 469.93 4.03 186 67 71 4 470.38 1.16 187 68 71 3 475.07 1.19 188 68 72 4 470.35 1.17 189 68 79 11 184.90 18.87 190 69 72 3 475.41 1.36 191 69 73 4 455.12 3.98 192 69 76 7 287.21 8.38 193 69 80 11 148.46 9.44 194 69 128 59 194.86 2.89 195 69 132 63 164.72 1.30 196 70 73 3 470.31 1.19 197 70 128 58 191.75 1.31 198 72 75 3 471.78 0.12 199 72 76 4 389.62 11.76 200 72 79 7 266.85 1.28 201 73 76 3 479.50 1.54 202 73 128 55 206.00 2.31 203 75 78 3 479.88 1.34 204 75 79 4 436.04 15.20 205 76 79 3 465.66 0.39 206 76 80 4 413.44 3.90 207 76 128 52 221.05 0.43 208 76 131 55 218.99 1.19 209 76 132 56 206.51 2.44 210 77 81 4 442.06 9.93 211 77 135 58 206.19 2.32 212 78 81 3 476.31 2.15 213 80 83 3 480.74 0.07 214 80 84 4 449.64 6.44 215 80 132 52 221.95 0.67 216 80 135 55 221.29 0.35 217 81 84 3 471.56 4.51 218 81 85 4 466.16 1.82 219 81 139 58 221.28 0.36 220 82 85 3 480.09 0.90 221 82 86 4 477.42 3.79 222 83 86 3 477.43 3.79 223 83 87 4 477.42 3.79 224 83 136 53 221.98 0.69 225 84 87 3 483.46 0.79 226 84 88 4 471.98 6.50 227 84 135 51 222.01 0.67 228 84 136 52 221.94 0.69 229 84 138 54 221.98 0.67 230 84 139 55 221.94 0.69 231 85 88 3 478.64 3.19 232 85 89 4 469.00 7.99 233 85 139 54 221.92 0.68 234 86 89 3 485.33 0.17 235 86 90 4 455.16 1.08 236 86 91 5 450.04 1.47 237 87 91 4 409.01 19.04 238 87 92 5 408.99 19.05 239 87 93 6 376.81 35.13 240 87 98 11 289.53 2.82 241 87 136 49 222.19 0.72 242 87 140 53 221.99 0.69 243 88 92 4 419.84 13.62 244 88 139 51 222.09 0.71 245 88 140 52 221.93 0.68 246 89 92 3 492.91 3.16 247 92 140 48 222.13 0.71 248 93 97 4 482.50 0.33 249 93 98 5 480.00 1.02 250 93 140 47 222.28 0.68 251 94 97 3 495.75 2.32 252 94 98 4 484.89 0.86 253 95 98 3 492.97 3.18 254 95 140 45 222.34 0.70 255 96 99 3 494.80 4.09 256 96 100 4 481.04 0.56 257 97 100 3 480.04 1.02 258 97 101 4 474.66 1.68 259 98 101 3 480.48 1.04 260 98 102 4 470.18 1.34 261 98 133 35 222.95 0.66 262 98 136 38 222.96 0.66 263 98 137 39 222.94 0.66 264 98 140 42 222.94 0.66 265 99 102 3 477.85 2.35 266 99 103 4 470.21 1.35 267 100 103 3 477.85 2.35 268 100 104 4 470.22 1.36 269 101 104 3 474.47 0.77 270 101 105 4 465.50 3.71 271 102 105 3 473.28 0.18 272 102 106 4 465.51 3.71 273 102 129 27 223.39 0.63 274 102 133 31 223.37 0.64 275 103 106 3 468.75 3.88 276 103 107 4 462.34 1.04 277 104 107 3 476.98 3.17 278 104 108 4 465.89 2.39 279 105 108 3 480.23 1.54 280 105 109 4 465.88 2.39 281 105 129 24 223.67 0.70 282 106 109 3 480.41 1.45 283 106 110 4 463.32 1.11 284 106 117 11 226.25 0.70 285 106 122 16 224.08 0.65 286 106 125 19 223.92 0.73 287 106 126 20 223.91 0.68 288 106 129 23 223.75 0.67 289 107 110 3 472.12 2.38 290 107 111 4 463.32 1.11 291 108 111 3 475.19 2.00 292 108 112 4 450.94 1.85 293 109 112 3 481.34 1.07 294 109 113 4 443.83 5.41 295 109 125 16 224.09 0.65 296 110 113 3 479.81 1.83 297 110 117 7 226.33 0.73 298 113 116 3 477.86 0.55 299 113 117 4 442.82 5.16 300 114 117 3 478.08 0.66 301 115 118 3 526.28 0.91 302 116 121 5 456.94 0.23 303 117 121 4 464.57 3.32 304 117 122 5 456.91 0.24 305 117 125 8 423.66 0.91 306 118 121 3 468.25 1.48 307 118 122 4 457.68 0.14 308 119 122 3 465.08 0.10 309 119 123 4 461.35 1.97 310 120 123 3 468.84 1.19 311 120 124 4 460.00 0.73 312 121 124 3 466.41 2.46 313 121 125 4 459.92 0.77 314 122 125 3 474.86 1.77 315 122 126 4 474.70 1.72 316 123 126 3 476.68 0.86 317 123 127 4 474.71 1.72 318 124 127 3 474.72 1.72 319 124 128 4 474.71 1.72 320 125 128 3 473.62 2.91 321 125 129 4 467.89 0.73 322 126 129 3 482.05 1.31 323 126 130 4 468.89 1.24 324 127 130 3 481.29 0.93 325 127 131 4 467.26 0.42 326 128 131 3 472.20 5.48 327 128 132 4 464.68 1.71 328 129 132 3 478.04 4.71 329 129 133 4 464.66 1.70 330 130 133 3 472.16 2.04 331 130 134 4 460.61 0.35 332 131 134 3 465.64 2.06 333 131 135 4 464.47 1.35 334 132 135 3 477.09 3.78 335 132 136 4 464.48 1.35 336 133 136 3 477.09 3.78 337 133 137 4 463.91 0.15 338 134 137 3 481.12 1.46 339 134 138 4 463.00 0.60 340 135 138 3 474.60 1.80 341 136 140 4 491.44 0.39 342 137 140 3 485.50 0.97