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 5 447.08 2.23 2 2 73 71 31.28 0.17 3 2 76 74 25.96 0.34 4 2 127 125 22.86 0.32 5 2 128 126 22.14 0.04 6 3 6 3 475.94 0.52 7 3 7 4 466.06 3.87 8 4 7 3 474.47 0.33 9 4 8 4 474.44 0.32 10 5 8 3 476.97 1.58 11 5 9 4 474.44 0.34 12 6 9 3 477.72 1.21 13 6 10 4 474.43 0.33 14 6 124 118 47.78 0.49 15 6 127 121 47.76 0.50 16 7 10 3 474.46 0.32 17 7 11 4 474.43 0.33 18 7 73 66 48.41 0.77 19 7 74 67 53.28 0.95 20 8 11 3 477.06 0.10 21 8 12 4 466.40 4.33 22 9 12 3 477.06 0.10 23 9 13 4 469.10 2.93 24 9 121 112 61.01 1.34 25 9 124 115 61.00 1.35 26 10 13 3 486.09 2.59 27 10 14 4 448.67 1.52 28 10 70 60 61.34 1.18 29 10 124 114 61.05 1.32 30 10 125 115 61.01 1.34 31 10 128 118 61.01 1.34 32 11 15 4 455.31 4.82 33 11 70 59 61.34 1.18 34 11 71 60 61.38 1.16 35 11 73 62 61.37 1.16 36 12 15 3 469.57 1.81 37 12 16 4 469.57 1.80 38 13 16 3 477.82 1.42 39 13 17 4 469.57 1.81 40 13 113 100 79.41 1.01 41 13 121 108 61.74 1.09 42 13 125 112 61.72 1.09 43 14 17 3 465.45 0.24 44 14 18 4 465.45 0.24 45 14 21 7 375.74 13.04 46 14 63 49 72.03 0.21 47 14 66 52 61.73 1.08 48 14 67 53 61.72 1.08 49 14 70 56 61.71 1.08 50 15 18 3 473.59 0.65 51 16 113 97 95.53 1.52 52 16 116 100 93.94 0.72 53 17 20 3 484.95 0.69 54 17 21 4 443.52 0.36 55 17 24 7 385.34 17.96 56 17 109 92 91.34 2.00 57 17 113 96 95.64 1.55 58 18 21 3 493.20 3.39 59 20 23 3 473.49 1.04 60 20 24 4 469.00 0.09 61 21 24 3 466.99 1.11 62 21 25 4 466.97 1.10 63 21 63 42 98.10 1.41 64 22 25 3 469.01 0.10 65 22 26 4 467.00 1.12 66 22 60 38 103.72 1.19 67 22 63 41 98.33 1.51 68 23 26 3 480.26 5.50 69 23 27 4 464.25 2.50 70 23 56 33 118.30 0.04 71 24 27 3 480.26 5.50 72 24 28 4 464.39 2.43 73 24 108 84 118.67 0.14 74 24 109 85 121.40 0.80 75 24 112 88 129.20 0.38 76 25 28 3 472.00 0.07 77 25 29 4 468.99 2.69 78 25 59 34 118.25 0.03 79 25 63 38 118.19 0.03 80 26 29 3 470.65 1.86 81 26 30 4 467.73 2.06 82 26 55 29 121.20 0.60 83 26 56 30 125.36 1.47 84 26 59 33 118.25 0.01 85 27 30 3 469.39 1.23 86 27 31 4 467.38 2.24 87 27 108 81 129.75 0.36 88 27 112 85 130.97 0.71 89 28 31 3 467.73 2.06 90 28 32 4 467.37 2.23 91 28 104 76 129.69 0.38 92 28 105 77 129.63 0.36 93 28 108 80 129.97 0.27 94 29 32 3 465.72 3.06 95 29 33 4 465.72 3.06 96 29 55 26 130.30 0.43 97 29 58 29 130.28 0.43 98 29 59 30 130.15 0.37 99 29 101 72 129.75 0.36 100 30 33 3 479.88 1.18 101 30 34 4 461.14 0.77 102 30 50 20 131.03 0.72 103 31 34 3 475.45 1.03 104 31 35 4 466.48 3.45 105 31 104 73 130.28 0.55 106 31 107 76 131.00 0.66 107 31 108 77 131.03 0.67 108 32 35 3 473.35 0.02 109 32 36 4 452.06 3.75 110 32 39 7 347.24 16.48 111 32 101 69 130.22 0.56 112 32 104 72 130.49 0.48 113 33 37 4 427.01 2.57 114 33 39 6 354.46 12.87 115 33 40 7 295.04 3.27 116 33 43 10 281.25 3.62 117 33 48 15 131.12 0.70 118 34 37 3 482.88 0.90 119 36 39 3 491.28 5.66 120 36 100 64 130.37 0.51 121 36 103 67 131.09 0.68 122 36 104 68 131.09 0.68 123 37 40 3 480.06 0.06 124 38 41 3 492.13 0.67 125 39 42 3 487.59 1.54 126 39 43 4 494.28 1.80 127 39 97 58 130.41 0.61 128 39 100 61 131.06 0.66 129 40 43 3 494.28 1.80 130 40 44 4 478.27 1.80 131 40 48 8 249.16 1.02 132 41 44 3 494.29 1.80 133 42 45 3 646.64 0.14 134 42 92 50 130.27 0.58 135 42 93 51 130.21 0.58 136 42 94 52 130.86 0.74 137 42 97 55 131.06 0.66 138 43 46 3 478.38 0.77 139 43 48 5 445.66 2.81 140 43 58 15 242.24 0.80 141 45 54 9 249.77 0.77 142 46 54 8 249.75 0.77 143 46 55 9 249.75 0.77 144 46 58 12 249.75 0.77 145 47 52 5 262.30 5.42 146 47 54 7 249.81 0.79 147 47 55 8 249.84 0.81 148 48 52 4 390.94 9.39 149 48 55 7 249.82 0.82 150 49 52 3 475.96 0.88 151 52 55 3 469.69 2.29 152 52 56 4 460.98 4.39 153 53 56 3 470.27 0.26 154 53 57 4 464.13 2.81 155 54 57 3 470.27 0.26 156 54 58 4 464.12 2.81 157 55 58 3 464.14 2.81 158 55 59 4 463.44 3.14 159 56 59 3 474.35 1.68 160 56 60 4 471.13 0.70 161 57 60 3 483.80 4.28 162 57 61 4 471.11 0.70 163 58 61 3 473.36 0.41 164 58 62 4 466.49 1.60 165 59 62 3 477.75 2.11 166 59 63 4 463.37 3.08 167 60 63 3 471.91 1.19 168 60 64 4 465.43 1.25 169 61 64 3 469.24 2.14 170 61 65 4 465.62 3.50 171 62 65 3 483.15 0.40 172 62 66 4 467.35 2.64 173 62 101 39 147.21 5.41 174 63 66 3 478.30 2.83 175 63 67 4 467.37 2.62 176 64 67 3 470.36 1.14 177 64 68 4 462.76 2.62 178 65 68 3 470.34 1.15 179 65 69 4 462.81 2.64 180 65 80 15 147.44 5.40 181 65 83 18 147.16 5.48 182 66 69 3 475.18 2.85 183 66 70 4 462.82 2.66 184 66 105 39 165.77 0.79 185 66 129 63 157.73 0.35 186 66 132 66 147.43 5.38 187 67 70 3 475.35 1.31 188 67 71 4 475.08 1.19 189 68 71 3 475.09 1.19 190 68 72 4 475.07 1.19 191 68 79 11 226.34 1.05 192 69 72 3 475.42 1.35 193 69 73 4 470.36 1.17 194 69 76 7 278.25 11.54 195 69 80 11 226.34 1.05 196 69 128 59 183.64 2.73 197 69 132 63 157.56 0.44 198 70 73 3 470.31 1.19 199 70 128 58 184.68 2.21 200 72 75 3 468.82 1.59 201 72 76 4 446.98 0.90 202 72 79 7 266.60 4.40 203 73 76 3 479.46 1.52 204 75 78 3 479.88 1.34 205 75 79 4 458.73 1.59 206 76 79 3 468.80 1.18 207 76 80 4 428.53 13.51 208 76 128 52 221.05 0.43 209 76 131 55 219.74 0.98 210 76 132 56 215.49 1.15 211 76 135 59 210.72 3.50 212 77 81 4 428.54 13.50 213 77 135 58 210.53 3.41 214 78 81 3 465.25 0.54 215 80 83 3 480.18 0.21 216 80 84 4 461.31 2.54 217 80 132 52 221.40 0.42 218 80 135 55 221.16 0.41 219 81 84 3 478.21 1.19 220 81 85 4 461.62 2.41 221 81 139 58 221.08 0.38 222 82 85 3 479.44 0.58 223 82 86 4 471.13 2.35 224 83 86 3 475.73 4.65 225 83 87 4 464.34 1.05 226 83 136 53 221.55 0.42 227 84 87 3 476.26 4.38 228 84 88 4 459.62 3.43 229 84 135 51 221.57 0.42 230 84 136 52 221.55 0.41 231 84 138 54 221.53 0.42 232 84 139 55 221.50 0.42 233 85 88 3 478.64 3.19 234 85 89 4 450.15 6.03 235 85 139 54 221.51 0.41 236 86 89 3 485.32 0.17 237 86 90 4 442.84 3.08 238 86 91 5 417.22 9.73 239 87 91 4 367.88 2.54 240 87 92 5 342.11 15.40 241 87 93 6 337.33 16.05 242 87 98 11 332.07 18.46 243 87 136 49 221.63 0.43 244 87 140 53 221.50 0.41 245 88 92 4 345.15 13.87 246 88 139 51 221.55 0.42 247 88 140 52 221.47 0.42 248 89 92 3 490.06 1.74 249 89 139 50 221.58 0.42 250 93 97 4 484.62 0.99 251 93 98 5 479.97 1.33 252 93 140 47 221.73 0.39 253 94 97 3 501.85 0.72 254 94 98 4 484.89 0.86 255 95 98 3 492.97 3.18 256 95 140 45 221.88 0.40 257 96 99 3 494.80 4.09 258 96 100 4 480.98 0.53 259 97 100 3 479.98 1.01 260 97 101 4 470.20 1.35 261 98 101 3 485.39 1.42 262 98 102 4 470.19 1.34 263 98 133 35 222.21 0.29 264 98 136 38 222.22 0.29 265 98 137 39 222.22 0.29 266 98 140 42 222.19 0.29 267 99 102 3 477.85 2.35 268 99 103 4 473.29 1.35 269 100 103 3 477.85 2.35 270 100 104 4 473.29 1.35 271 101 104 3 472.16 2.83 272 101 105 4 463.61 1.31 273 102 105 3 463.75 1.38 274 102 106 4 461.72 0.36 275 102 129 27 222.71 0.13 276 102 133 31 222.65 0.16 277 103 106 3 470.84 0.29 278 103 107 4 464.43 0.93 279 104 107 3 472.94 5.18 280 104 108 4 464.43 0.93 281 105 108 3 480.23 1.54 282 105 109 4 469.66 1.68 283 105 129 24 223.27 0.36 284 106 109 3 481.26 1.02 285 106 110 4 469.65 1.68 286 106 117 11 238.91 7.34 287 106 122 16 224.03 0.16 288 106 125 19 223.88 0.23 289 106 126 20 223.80 0.23 290 106 129 23 223.79 0.23 291 107 110 3 474.68 3.66 292 107 111 4 467.79 2.60 293 108 111 3 474.68 3.66 294 108 112 4 467.73 2.67 295 109 112 3 477.53 2.23 296 109 113 4 448.20 3.63 297 109 125 16 224.01 0.20 298 110 113 3 479.81 1.83 299 110 117 7 239.22 7.48 300 113 116 3 477.86 0.55 301 113 117 4 469.31 3.72 302 114 117 3 480.09 1.67 303 115 118 3 526.28 0.91 304 116 121 5 452.18 2.16 305 117 121 4 463.85 3.68 306 117 122 5 452.16 2.16 307 117 125 8 420.36 10.54 308 118 121 3 468.25 1.48 309 118 122 4 458.28 0.13 310 119 122 3 468.25 1.48 311 119 123 4 461.91 1.69 312 120 123 3 473.83 1.31 313 120 124 4 463.10 1.48 314 121 124 3 474.30 1.92 315 121 125 4 459.13 0.51 316 122 125 3 474.83 1.78 317 122 126 4 462.72 1.28 318 123 126 3 474.82 1.78 319 123 127 4 465.60 2.84 320 124 127 3 474.72 1.72 321 124 128 4 465.86 0.28 322 125 128 3 475.35 2.04 323 125 129 4 467.88 0.73 324 126 129 3 480.37 2.15 325 126 130 4 468.89 1.24 326 127 130 3 475.13 4.01 327 127 131 4 468.89 1.24 328 128 131 3 475.13 4.01 329 128 132 4 465.61 2.08 330 129 132 3 478.04 4.71 331 129 133 4 461.28 0.06 332 130 133 3 476.79 3.50 333 130 134 4 461.28 0.06 334 131 134 3 465.67 2.06 335 131 135 4 465.67 2.05 336 132 135 3 477.09 3.78 337 132 136 4 464.37 1.40 338 133 136 3 477.09 3.78 339 133 137 4 462.60 0.50 340 134 137 3 473.63 0.45 341 134 138 4 460.39 0.60 342 135 138 3 472.08 1.22 343 136 140 4 489.82 1.20 344 137 140 3 485.50 0.97