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 5 463.00 0.63 2 2 73 71 35.31 1.53 3 2 76 74 32.54 0.20 4 2 127 125 25.84 1.31 5 2 128 126 25.57 1.11 6 3 6 3 476.29 1.14 7 3 7 4 463.66 0.61 8 4 7 3 477.88 0.34 9 4 8 4 474.18 1.52 10 5 8 3 474.19 1.52 11 5 9 4 466.47 2.34 12 6 9 3 475.29 1.92 13 6 10 4 468.42 1.19 14 6 124 118 50.88 0.01 15 6 127 121 52.62 0.85 16 7 10 3 480.31 4.24 17 7 11 4 477.41 5.69 18 7 73 66 53.22 0.56 19 7 74 67 53.37 0.64 20 8 11 3 479.42 4.69 21 8 12 4 468.41 1.20 22 9 12 3 477.64 5.82 23 9 13 4 476.63 6.08 24 9 121 112 59.43 3.48 25 9 124 115 59.38 3.50 26 10 13 3 485.81 1.49 27 10 14 4 467.62 1.58 28 10 70 60 59.39 3.50 29 10 124 114 59.41 3.50 30 10 125 115 59.41 3.50 31 10 128 118 59.36 3.50 32 11 14 3 481.57 3.83 33 11 15 4 466.28 0.93 34 11 70 59 59.37 3.52 35 11 73 62 59.37 3.52 36 12 15 3 478.75 2.18 37 12 16 4 474.79 4.16 38 13 16 3 483.96 0.43 39 13 17 4 473.54 4.78 40 13 121 108 59.77 3.56 41 13 125 112 59.72 3.58 42 14 17 3 470.17 1.03 43 14 18 4 464.74 1.71 44 14 21 7 394.69 1.45 45 14 63 49 64.17 2.87 46 14 66 52 59.71 3.59 47 14 67 53 59.71 3.59 48 14 70 56 59.70 3.60 49 15 18 3 484.76 2.89 50 16 113 97 75.39 0.24 51 16 116 100 74.79 0.54 52 17 20 3 484.04 1.19 53 17 21 4 454.25 4.54 54 17 24 7 396.15 2.95 55 17 109 92 74.88 0.49 56 17 113 96 75.40 0.24 57 18 21 3 494.94 0.71 58 20 23 3 482.87 1.95 59 20 24 4 474.49 0.89 60 21 24 3 483.67 1.54 61 21 25 4 474.51 0.89 62 21 63 42 91.46 6.45 63 22 25 3 483.67 1.54 64 22 26 4 478.45 1.06 65 22 60 38 101.88 1.25 66 22 63 41 101.87 1.26 67 23 26 3 483.67 1.54 68 23 27 4 474.53 0.90 69 24 27 3 474.51 0.93 70 24 28 4 474.50 0.92 71 24 108 84 127.20 1.13 72 24 109 85 128.31 0.08 73 24 112 88 133.88 0.01 74 25 28 3 481.58 2.58 75 25 29 4 474.53 0.93 76 25 59 34 123.37 0.62 77 26 29 3 484.32 1.21 78 26 30 4 474.51 0.92 79 26 55 29 133.22 0.02 80 26 56 30 130.46 0.93 81 26 59 33 123.43 0.65 82 27 30 3 490.34 7.00 83 27 31 4 471.85 0.41 84 27 108 81 134.37 0.14 85 27 112 85 135.22 0.36 86 28 31 3 486.58 0.94 87 28 32 4 466.75 2.14 88 28 101 73 134.23 0.08 89 28 104 76 134.27 0.10 90 28 105 77 134.25 0.10 91 28 108 80 134.40 0.14 92 29 32 3 473.02 1.02 93 29 33 4 466.14 0.03 94 29 55 26 135.03 0.40 95 29 58 29 134.97 0.41 96 29 59 30 134.34 0.09 97 29 62 33 134.34 0.10 98 29 101 72 134.29 0.10 99 30 33 3 488.25 1.26 100 30 34 4 464.93 1.02 101 30 50 20 135.21 0.38 102 31 34 3 488.25 1.25 103 31 35 4 464.49 0.85 104 31 104 73 134.38 0.14 105 31 107 76 135.16 0.34 106 31 108 77 135.16 0.35 107 32 35 3 488.25 1.25 108 32 36 4 456.61 0.32 109 32 39 7 337.10 11.47 110 32 100 68 134.30 0.11 111 32 101 69 134.38 0.15 112 32 104 72 134.71 0.27 113 33 37 4 441.28 3.07 114 33 39 6 337.10 11.47 115 33 40 7 292.32 0.43 116 33 43 10 285.75 3.71 117 33 48 15 177.25 20.63 118 33 55 22 135.26 0.36 119 34 37 3 490.58 3.95 120 36 39 3 497.50 0.01 121 36 100 64 134.40 0.16 122 36 103 67 135.27 0.36 123 36 104 68 135.27 0.36 124 37 40 3 494.12 1.68 125 38 41 3 503.99 2.62 126 39 42 3 497.25 0.76 127 39 43 4 491.88 1.93 128 39 97 58 134.39 0.17 129 39 100 61 135.16 0.35 130 40 43 3 492.50 0.92 131 40 48 8 237.06 4.88 132 41 44 3 505.91 1.50 133 42 45 3 652.50 0.00 134 42 93 51 134.31 0.16 135 42 94 52 134.78 0.31 136 42 97 55 135.17 0.35 137 43 46 3 486.88 1.65 138 43 48 5 440.35 11.31 139 43 58 15 178.62 21.25 140 46 54 8 246.25 1.41 141 46 58 12 246.21 1.39 142 47 52 5 313.11 4.33 143 47 54 7 255.01 1.56 144 47 55 8 255.00 1.56 145 48 52 4 422.52 4.76 146 48 55 7 255.01 1.56 147 49 52 3 475.88 3.10 148 52 55 3 477.06 2.02 149 52 56 4 476.94 2.83 150 53 56 3 477.81 2.40 151 53 57 4 469.64 0.82 152 54 57 3 495.92 3.41 153 54 58 4 485.00 2.04 154 55 58 3 485.03 2.04 155 55 59 4 485.01 2.04 156 56 59 3 487.66 1.92 157 56 60 4 485.03 2.04 158 57 60 3 486.47 1.32 159 57 61 4 485.03 2.04 160 58 61 3 484.99 2.02 161 58 62 4 484.98 2.02 162 59 62 3 473.23 2.96 163 59 63 4 474.56 1.46 164 60 63 3 474.59 1.47 165 60 64 4 474.63 1.48 166 61 64 3 488.31 1.58 167 61 65 4 474.63 1.48 168 62 65 3 480.01 0.48 169 62 66 4 474.63 1.48 170 63 66 3 476.05 1.51 171 63 67 4 474.62 1.48 172 64 67 3 476.65 0.47 173 64 68 4 474.25 1.66 174 65 68 3 479.34 0.89 175 65 69 4 474.25 1.66 176 65 80 15 154.17 2.10 177 65 83 18 154.11 2.08 178 66 69 3 474.26 1.66 179 66 70 4 474.25 1.66 180 66 105 39 156.66 1.36 181 66 129 63 155.84 1.35 182 66 132 66 154.34 2.10 183 67 70 3 474.10 1.59 184 67 71 4 473.89 1.70 185 68 71 3 475.40 0.94 186 68 72 4 473.88 1.69 187 68 79 11 193.03 19.23 188 69 72 3 472.65 0.45 189 69 73 4 461.36 4.58 190 69 76 7 284.37 1.97 191 69 80 11 199.31 15.61 192 69 128 59 165.49 2.30 193 69 132 63 155.36 1.97 194 70 73 3 469.11 0.71 195 70 128 58 179.39 4.65 196 72 75 3 486.08 3.40 197 72 76 4 453.43 3.91 198 72 79 7 304.76 15.35 199 73 76 3 475.85 1.72 200 75 78 3 489.23 0.85 201 75 79 4 468.18 2.19 202 76 79 3 476.13 5.70 203 76 80 4 408.61 0.12 204 76 128 52 204.47 2.90 205 76 131 55 203.41 2.58 206 76 132 56 201.64 1.82 207 76 135 59 201.19 1.85 208 77 81 4 395.97 9.04 209 77 135 58 201.19 1.85 210 78 81 3 471.97 1.01 211 80 83 3 486.72 2.91 212 80 84 4 474.74 0.35 213 80 132 52 205.17 2.60 214 80 135 55 204.63 2.81 215 80 136 56 204.63 2.81 216 81 84 3 485.73 3.40 217 81 85 4 481.12 0.22 218 82 85 3 482.29 0.56 219 82 86 4 481.12 0.22 220 83 86 3 481.12 0.22 221 83 87 4 474.64 1.22 222 83 136 53 205.28 2.68 223 84 87 3 483.51 0.97 224 84 88 4 472.13 0.38 225 84 135 51 205.27 2.66 226 84 136 52 205.25 2.66 227 84 139 55 205.19 2.68 228 85 88 3 482.24 0.34 229 85 89 4 440.78 4.81 230 85 90 5 433.43 2.19 231 85 139 54 205.22 2.66 232 86 90 4 417.17 4.08 233 86 91 5 417.16 4.08 234 87 91 4 378.74 15.10 235 87 92 5 378.70 15.08 236 87 93 6 355.56 26.59 237 87 98 11 278.28 0.96 238 87 136 49 205.40 2.69 239 88 92 4 367.22 20.82 240 88 139 51 205.30 2.68 241 88 140 52 205.29 2.69 242 89 92 3 481.44 0.18 243 89 139 50 205.34 2.66 244 92 140 48 205.49 2.66 245 93 97 4 488.32 2.12 246 93 98 5 478.52 0.67 247 93 140 47 205.74 2.69 248 94 97 3 489.35 1.61 249 94 98 4 490.06 1.97 250 95 98 3 490.55 2.21 251 95 137 42 206.27 2.61 252 95 140 45 205.91 2.75 253 96 99 3 490.07 1.97 254 96 100 4 489.05 2.49 255 97 100 3 487.11 3.46 256 97 101 4 485.32 4.35 257 98 101 3 489.74 2.15 258 98 102 4 472.45 0.56 259 98 133 35 206.88 2.49 260 98 136 38 206.90 2.48 261 98 137 39 206.90 2.48 262 99 102 3 489.74 2.15 263 99 103 4 469.79 1.90 264 100 103 3 476.37 0.29 265 100 104 4 465.56 4.01 266 101 104 3 473.83 0.12 267 101 105 4 465.56 4.01 268 102 105 3 477.57 1.28 269 102 106 4 470.55 1.53 270 102 129 27 207.31 2.61 271 102 133 31 207.30 2.62 272 103 106 3 474.67 1.80 273 103 107 4 465.70 0.90 274 104 107 3 470.40 3.25 275 104 108 4 465.69 0.90 276 105 108 3 475.96 5.33 277 105 109 4 471.54 2.27 278 105 129 24 208.38 2.31 279 106 109 3 479.18 3.71 280 106 110 4 471.56 2.26 281 106 117 11 215.92 2.96 282 106 122 16 208.67 2.34 283 106 125 19 208.46 2.29 284 106 126 20 208.43 2.31 285 106 129 23 208.40 2.31 286 107 110 3 476.45 2.35 287 107 111 4 473.93 1.07 288 108 111 3 480.84 2.38 289 108 112 4 473.92 1.07 290 109 112 3 473.91 1.07 291 109 113 4 449.49 8.77 292 109 125 16 209.77 2.50 293 110 117 7 236.62 8.22 294 113 116 3 475.17 1.23 295 113 117 4 455.23 3.94 296 114 117 3 488.42 1.88 297 115 118 3 522.46 0.31 298 116 121 5 445.89 7.36 299 117 122 5 422.44 4.37 300 117 125 8 372.16 1.55 301 118 121 3 480.00 2.21 302 118 122 4 466.75 3.07 303 119 122 3 480.00 2.21 304 119 123 4 468.12 2.39 305 120 123 3 475.30 0.62 306 120 124 4 468.12 2.39 307 121 124 3 469.88 2.08 308 121 125 4 468.12 2.39 309 122 125 3 477.72 0.74 310 122 126 4 467.19 1.89 311 123 126 3 472.24 1.41 312 123 127 4 469.13 2.31 313 124 127 3 471.95 1.27 314 124 128 4 471.59 1.08 315 125 128 3 471.95 1.26 316 125 129 4 468.60 2.58 317 126 129 3 482.78 0.73 318 126 130 4 468.60 2.56 319 127 130 3 469.19 2.27 320 127 131 4 468.67 1.20 321 128 131 3 473.66 3.25 322 128 132 4 475.93 0.96 323 129 132 3 476.79 1.39 324 129 133 4 470.13 1.93 325 130 133 3 475.94 0.96 326 130 134 4 470.15 1.94 327 131 134 3 480.80 1.47 328 131 135 4 470.14 1.95 329 132 135 3 476.57 0.07 330 132 136 4 469.82 2.11 331 133 136 3 480.80 1.47 332 133 137 4 475.20 0.58 333 134 137 3 483.74 1.26 334 134 138 4 454.92 4.00 335 135 138 3 469.19 2.43 336 137 140 3 490.71 2.14 337 137 141 4 480.57 2.73 338 138 141 3 485.09 0.47