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 5 448.60 5.32 2 2 73 71 28.84 0.30 3 2 76 74 28.71 0.24 4 2 127 125 23.66 0.22 5 2 128 126 23.64 0.23 6 2 131 129 23.63 0.23 7 3 6 3 473.43 1.31 8 3 7 4 466.06 2.38 9 4 7 3 476.75 0.35 10 4 8 4 465.64 1.82 11 5 8 3 478.52 1.24 12 5 9 4 462.24 0.36 13 6 9 3 478.23 0.29 14 6 10 4 462.24 0.36 15 6 124 118 46.96 0.36 16 6 127 121 46.96 0.36 17 7 10 3 479.81 0.17 18 7 11 4 470.81 3.93 19 7 73 66 47.45 0.26 20 7 74 67 47.45 0.26 21 8 11 3 483.54 1.69 22 8 12 4 470.86 3.91 23 9 12 3 483.71 1.60 24 9 13 4 470.86 3.90 25 9 121 112 62.97 0.36 26 9 124 115 61.59 0.01 27 10 13 3 479.59 0.46 28 10 14 4 470.86 3.89 29 10 70 60 62.62 0.53 30 10 124 114 62.97 0.36 31 10 125 115 62.95 0.36 32 10 128 118 61.59 0.01 33 11 14 3 478.04 0.65 34 11 15 4 470.85 3.89 35 11 70 59 61.86 0.14 36 11 73 62 62.72 0.49 37 12 15 3 479.11 1.35 38 12 16 4 470.95 3.82 39 13 16 3 478.54 3.48 40 13 17 4 473.99 1.21 41 13 113 100 76.39 1.83 42 13 121 108 64.58 0.25 43 13 125 112 64.54 0.26 44 14 17 3 472.81 1.79 45 14 18 4 466.25 1.48 46 14 21 7 391.79 13.13 47 14 63 49 64.62 0.29 48 14 66 52 64.56 0.26 49 14 67 53 64.55 0.26 50 14 70 56 64.55 0.26 51 14 109 95 76.27 1.88 52 15 18 3 469.31 0.05 53 16 113 97 89.08 0.19 54 16 116 100 83.94 1.40 55 17 20 3 482.67 1.94 56 17 21 4 443.00 12.47 57 17 24 7 380.25 18.91 58 17 109 92 84.39 2.16 59 18 21 3 488.64 0.93 60 20 23 3 485.62 0.58 61 20 24 4 472.20 0.10 62 21 24 3 473.13 0.36 63 21 25 4 472.22 0.10 64 21 63 42 99.28 0.21 65 22 25 3 479.32 1.28 66 22 26 4 472.22 0.10 67 22 59 37 108.20 1.18 68 22 60 38 105.72 0.03 69 22 63 41 105.57 0.12 70 23 26 3 485.83 1.98 71 23 27 4 472.19 0.12 72 24 27 3 472.19 0.12 73 24 28 4 467.23 2.35 74 24 108 84 118.41 0.96 75 24 112 88 136.62 1.02 76 25 28 3 473.60 0.09 77 25 29 4 465.43 1.34 78 25 59 34 113.73 0.24 79 25 63 38 113.05 0.11 80 26 29 3 474.28 0.25 81 26 30 4 465.69 1.47 82 26 55 29 136.59 1.47 83 26 56 30 136.59 1.47 84 26 59 33 119.52 0.79 85 27 30 3 466.30 1.16 86 27 31 4 469.01 0.45 87 27 108 81 137.28 1.29 88 27 112 85 137.82 1.28 89 28 31 3 476.96 4.15 90 28 32 4 469.29 0.31 91 28 101 73 137.21 1.30 92 28 104 76 137.25 1.30 93 28 105 77 137.22 1.29 94 28 108 80 137.49 1.40 95 29 32 3 469.30 0.31 96 29 33 4 469.03 0.18 97 29 55 26 137.75 1.28 98 29 58 29 137.52 1.39 99 29 59 30 137.16 1.25 100 29 101 72 137.24 1.29 101 30 33 3 488.67 1.72 102 30 34 4 469.30 0.32 103 30 50 20 138.62 1.22 104 31 34 3 485.18 3.46 105 31 35 4 469.29 0.32 106 31 104 73 137.87 1.30 107 31 107 76 138.08 1.21 108 31 108 77 138.13 1.18 109 31 111 80 138.55 1.19 110 32 35 3 482.49 2.11 111 32 36 4 454.97 3.62 112 32 39 7 404.19 11.52 113 32 100 68 137.84 1.29 114 32 101 69 137.85 1.29 115 32 104 72 138.05 1.22 116 33 36 3 475.24 1.52 117 33 37 4 454.89 3.65 118 33 39 6 331.53 7.20 119 33 40 7 315.72 11.50 120 33 43 10 295.38 1.33 121 33 48 15 138.74 1.22 122 33 55 22 138.65 1.22 123 34 37 3 488.42 1.83 124 36 39 3 494.86 0.34 125 36 100 64 137.87 1.29 126 36 103 67 138.39 1.20 127 36 104 68 138.40 1.20 128 37 40 3 482.38 2.81 129 38 41 3 490.84 1.42 130 39 42 3 493.11 0.78 131 39 43 4 489.78 1.95 132 39 97 58 137.85 1.28 133 39 100 61 138.37 1.21 134 40 43 3 485.56 0.50 135 40 44 4 483.50 1.53 136 40 48 8 218.11 37.91 137 41 44 3 497.80 0.55 138 42 45 3 648.24 0.24 139 42 93 51 137.83 1.30 140 42 94 52 138.16 1.18 141 42 97 55 138.35 1.20 142 43 46 3 489.49 2.11 143 43 48 5 426.98 1.32 144 43 58 15 139.10 1.38 145 45 54 9 140.13 1.19 146 46 54 8 140.09 1.19 147 46 55 9 140.09 1.19 148 46 58 12 140.08 1.19 149 47 52 5 218.56 37.73 150 47 54 7 140.18 1.22 151 47 55 8 140.25 1.23 152 48 55 7 140.25 1.22 153 49 52 3 467.67 2.65 154 52 55 3 481.45 1.66 155 52 56 4 464.04 0.10 156 53 56 3 472.38 1.00 157 53 57 4 465.80 0.80 158 54 57 3 476.95 1.19 159 54 58 4 467.96 1.88 160 55 58 3 477.51 0.15 161 55 59 4 468.44 1.64 162 56 59 3 487.92 4.53 163 56 60 4 469.22 1.27 164 57 60 3 474.59 2.14 165 57 61 4 473.21 2.83 166 58 61 3 479.44 0.29 167 58 62 4 469.68 1.04 168 59 62 3 481.20 1.18 169 59 63 4 470.08 1.25 170 60 63 3 471.12 0.73 171 60 64 4 467.70 0.05 172 61 64 3 479.29 1.48 173 61 65 4 467.62 0.02 174 62 65 3 479.30 1.48 175 62 66 4 471.82 2.25 176 62 101 39 158.15 3.52 177 63 66 3 473.02 1.66 178 63 67 4 471.82 2.25 179 64 67 3 472.48 2.58 180 64 68 4 471.82 2.25 181 65 68 3 471.81 2.25 182 65 69 4 471.81 2.25 183 65 83 18 157.69 3.31 184 66 69 3 474.48 0.92 185 66 70 4 478.32 1.01 186 66 105 39 168.38 2.41 187 66 128 62 198.38 8.74 188 66 129 63 163.64 3.70 189 66 132 66 159.60 3.04 190 67 70 3 478.29 1.02 191 67 71 4 469.99 1.39 192 68 71 3 479.32 2.95 193 68 72 4 470.27 1.26 194 68 79 11 203.75 24.43 195 68 80 12 159.59 3.05 196 69 72 3 470.45 1.34 197 69 73 4 468.76 2.00 198 69 76 7 261.81 7.94 199 69 80 11 159.59 3.05 200 69 128 59 213.50 1.22 201 69 132 63 163.72 3.65 202 70 73 3 469.32 2.29 203 70 128 58 213.52 1.22 204 72 75 3 477.43 2.38 205 72 76 4 437.40 5.23 206 72 79 7 278.00 8.28 207 73 76 3 480.92 2.38 208 75 78 3 488.66 0.72 209 75 79 4 460.17 0.24 210 76 79 3 461.70 1.01 211 76 80 4 452.70 3.49 212 76 128 52 237.44 5.55 213 76 131 55 236.30 5.67 214 76 132 56 233.02 4.16 215 76 135 59 232.96 4.19 216 77 81 4 452.68 3.48 217 77 135 58 232.96 4.19 218 78 81 3 464.00 2.17 219 80 83 3 470.78 1.67 220 80 84 4 466.09 4.03 221 80 132 52 239.22 4.87 222 80 135 55 239.06 4.79 223 80 136 56 239.06 4.79 224 81 84 3 486.21 5.38 225 81 85 4 466.10 4.02 226 81 139 58 239.08 4.79 227 82 85 3 473.59 0.29 228 82 86 4 473.57 0.28 229 83 86 3 473.75 0.21 230 83 87 4 473.57 0.28 231 83 136 53 239.31 4.82 232 84 87 3 476.81 1.42 233 84 88 4 459.20 7.46 234 84 135 51 239.31 4.82 235 84 136 52 239.29 4.82 236 84 139 55 239.28 4.82 237 85 88 3 474.39 0.71 238 85 89 4 457.25 7.71 239 85 139 54 239.28 4.82 240 86 89 3 472.24 0.97 241 86 90 4 446.67 4.21 242 86 91 5 427.17 5.53 243 87 91 4 399.38 19.42 244 87 92 5 341.63 9.44 245 87 93 6 341.62 9.43 246 87 98 11 269.28 0.58 247 87 136 49 239.36 4.83 248 87 140 53 239.28 4.82 249 88 92 4 399.36 19.41 250 88 139 51 239.28 4.82 251 88 140 52 239.27 4.82 252 89 92 3 495.78 0.54 253 92 140 48 239.37 4.82 254 93 97 4 473.88 1.96 255 93 98 5 469.18 2.30 256 93 140 47 239.59 4.76 257 94 97 3 491.82 1.49 258 95 98 3 485.92 2.10 259 95 137 42 240.00 4.62 260 95 140 45 239.84 4.68 261 96 99 3 488.88 1.00 262 96 100 4 478.76 1.35 263 97 100 3 478.76 1.34 264 97 101 4 478.76 1.35 265 98 101 3 483.92 3.48 266 98 102 4 472.50 4.48 267 98 133 35 240.34 4.70 268 98 136 38 240.40 4.70 269 98 137 39 240.36 4.70 270 98 140 42 240.37 4.70 271 99 102 3 481.82 0.18 272 99 103 4 465.63 1.01 273 100 103 3 478.39 2.78 274 100 104 4 464.86 0.62 275 101 104 3 485.84 1.83 276 101 105 4 465.38 0.36 277 102 105 3 478.82 1.69 278 102 106 4 464.85 0.62 279 102 129 27 240.93 4.54 280 102 133 31 240.79 4.51 281 103 106 3 475.24 0.11 282 103 107 4 459.93 1.89 283 104 107 3 467.10 4.16 284 104 108 4 459.92 1.90 285 105 108 3 465.58 4.73 286 105 109 4 473.68 0.68 287 105 129 24 241.79 4.58 288 106 109 3 473.69 0.68 289 106 110 4 473.69 0.68 290 106 117 11 242.90 4.76 291 106 122 16 242.58 4.73 292 106 125 19 242.01 4.52 293 106 126 20 241.97 4.50 294 106 129 23 241.93 4.55 295 107 110 3 473.69 0.68 296 107 111 4 473.69 0.68 297 108 111 3 478.88 1.91 298 108 112 4 473.69 0.68 299 109 112 3 476.23 5.79 300 109 113 4 455.85 3.60 301 109 125 16 242.52 4.70 302 110 113 3 470.37 2.87 303 110 117 7 242.93 4.75 304 113 116 3 454.30 1.56 305 113 117 4 376.74 3.37 306 115 118 3 518.29 2.41 307 116 121 5 444.73 6.43 308 117 121 4 448.73 4.44 309 117 122 5 442.57 5.16 310 117 125 8 405.99 11.92 311 118 121 3 460.09 2.15 312 118 122 4 451.48 3.78 313 119 122 3 468.81 2.21 314 119 123 4 457.35 0.84 315 120 123 3 469.76 2.69 316 120 124 4 458.82 2.78 317 121 124 3 461.00 1.69 318 121 125 4 453.53 2.06 319 122 125 3 477.43 0.14 320 122 126 4 457.11 0.75 321 123 126 3 470.28 2.56 322 123 127 4 457.11 0.74 323 124 127 3 466.40 1.63 324 124 128 4 460.38 2.38 325 125 128 3 462.64 3.51 326 125 129 4 464.62 0.26 327 126 129 3 473.62 0.92 328 126 130 4 464.13 2.86 329 127 130 3 469.29 0.28 330 127 131 4 461.37 1.48 331 128 131 3 475.56 2.85 332 128 132 4 460.35 1.98 333 129 132 3 463.13 3.33 334 129 133 4 460.44 1.94 335 130 133 3 468.46 2.08 336 130 134 4 457.26 0.35 337 131 134 3 465.30 3.67 338 131 135 4 461.01 1.52 339 132 135 3 471.34 0.65 340 132 136 4 461.04 1.52 341 133 136 3 469.70 2.81 342 133 137 4 461.05 1.52 343 134 137 3 498.50 2.16 344 134 138 4 461.04 1.51 345 135 138 3 460.68 1.99 346 136 140 4 484.03 1.03 347 137 140 3 479.76 1.19