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 5 456.39 1.89 2 2 73 71 31.22 0.42 3 2 76 74 31.20 0.42 4 2 127 125 24.50 0.45 5 2 128 126 22.82 0.17 6 2 131 129 22.52 0.02 7 3 6 3 461.86 0.80 8 3 7 4 461.99 1.35 9 4 7 3 482.59 2.50 10 4 8 4 463.38 1.53 11 5 8 3 481.56 2.35 12 5 9 4 463.38 1.53 13 6 9 3 482.22 2.69 14 6 10 4 465.76 0.33 15 6 124 118 47.63 0.18 16 6 127 121 47.63 0.18 17 7 10 3 491.39 2.56 18 7 11 4 476.49 0.40 19 7 73 66 47.68 0.18 20 7 74 67 47.69 0.18 21 8 11 3 491.39 2.55 22 8 12 4 473.72 0.98 23 9 12 3 483.34 1.48 24 9 13 4 473.72 0.98 25 9 120 111 63.77 0.18 26 9 121 112 63.77 0.18 27 9 124 115 63.76 0.17 28 10 13 3 483.35 1.47 29 10 14 4 467.20 2.27 30 10 70 60 63.63 0.12 31 10 124 114 63.77 0.17 32 10 125 115 63.75 0.18 33 10 128 118 63.70 0.17 34 11 14 3 476.23 2.09 35 11 15 4 466.45 1.88 36 11 70 59 63.70 0.15 37 11 73 62 63.71 0.15 38 12 15 3 476.23 2.09 39 12 16 4 468.65 1.69 40 13 16 3 471.54 0.50 41 13 17 4 464.00 0.64 42 13 113 100 76.36 1.36 43 13 121 108 64.47 0.18 44 13 125 112 64.38 0.16 45 14 17 3 470.55 2.03 46 14 18 4 471.17 3.00 47 14 21 7 404.07 1.66 48 14 63 49 71.42 1.93 49 14 66 52 64.35 0.18 50 14 67 53 64.35 0.18 51 14 70 56 64.34 0.18 52 14 109 95 74.49 0.80 53 15 18 3 471.18 3.00 54 16 113 97 84.17 2.52 55 16 116 100 80.86 0.87 56 17 20 3 484.43 2.03 57 17 21 4 458.81 2.94 58 17 24 7 440.79 5.08 59 17 109 92 80.83 0.87 60 18 21 3 490.57 2.75 61 20 23 3 472.61 1.90 62 20 24 4 469.37 1.91 63 21 24 3 470.98 2.71 64 21 25 4 465.88 0.17 65 21 63 42 98.27 1.49 66 22 25 3 471.04 1.10 67 22 26 4 464.64 0.45 68 22 59 37 101.53 0.07 69 22 60 38 99.67 0.92 70 22 63 41 99.65 0.94 71 23 26 3 477.54 1.05 72 23 27 4 470.94 3.56 73 24 27 3 471.64 3.21 74 24 28 4 464.24 0.21 75 24 108 84 119.83 0.06 76 24 109 85 125.22 2.64 77 24 112 88 128.72 1.52 78 25 28 3 477.54 0.27 79 25 29 4 463.73 0.06 80 25 59 34 115.97 0.76 81 26 29 3 480.81 1.37 82 26 30 4 462.45 0.70 83 26 55 29 126.76 0.58 84 26 56 30 126.70 0.56 85 26 59 33 121.11 0.58 86 27 30 3 479.48 1.24 87 27 31 4 462.45 0.70 88 27 108 81 129.15 1.40 89 27 112 85 129.83 1.42 90 28 31 3 471.43 0.76 91 28 32 4 465.59 2.16 92 28 101 73 128.75 1.54 93 28 104 76 128.77 1.54 94 28 105 77 128.75 1.54 95 28 108 80 129.19 1.40 96 29 32 3 475.50 2.79 97 29 33 4 462.94 0.83 98 29 55 26 129.56 1.47 99 29 58 29 129.53 1.47 100 29 59 30 129.39 1.53 101 29 101 72 128.81 1.54 102 30 33 3 479.07 1.01 103 30 34 4 465.62 2.17 104 30 50 20 130.06 1.34 105 31 34 3 494.65 2.84 106 31 35 4 470.06 0.06 107 31 104 73 128.91 1.53 108 31 107 76 129.90 1.30 109 31 108 77 129.93 1.31 110 32 35 3 477.24 0.09 111 32 36 4 461.29 4.57 112 32 39 7 310.64 0.54 113 32 100 68 128.88 1.52 114 32 101 69 128.88 1.51 115 32 104 72 129.56 1.21 116 33 37 4 435.30 1.36 117 33 39 6 314.01 2.21 118 33 40 7 288.42 10.58 119 33 43 10 257.47 2.99 120 33 48 15 130.25 1.42 121 33 55 22 130.27 1.45 122 34 37 3 484.57 1.63 123 36 39 3 492.93 0.44 124 36 100 64 128.93 1.53 125 36 103 67 130.19 1.41 126 36 104 68 130.21 1.41 127 37 40 3 479.47 0.80 128 38 41 3 488.44 2.65 129 39 42 3 495.73 4.16 130 39 97 58 128.91 1.52 131 39 100 61 130.17 1.42 132 40 43 3 482.05 3.35 133 40 48 8 243.51 0.66 134 41 44 3 491.06 1.15 135 42 93 51 129.36 1.67 136 42 94 52 130.06 1.40 137 42 97 55 130.19 1.42 138 43 46 3 482.94 1.14 139 43 48 5 426.31 18.47 140 43 58 15 183.16 24.91 141 45 54 9 250.60 3.71 142 46 54 8 239.86 1.66 143 47 52 5 290.81 16.32 144 47 54 7 250.57 3.70 145 47 55 8 250.56 3.69 146 48 52 4 421.12 17.43 147 48 55 7 250.50 3.71 148 49 52 3 476.59 1.95 149 52 55 3 483.66 2.99 150 52 56 4 465.00 4.32 151 53 56 3 472.99 0.33 152 53 57 4 465.81 3.91 153 54 57 3 481.63 3.99 154 54 58 4 469.60 1.41 155 55 58 3 473.03 0.30 156 55 59 4 469.59 1.41 157 56 59 3 477.30 1.83 158 56 60 4 468.27 2.07 159 57 60 3 482.13 3.62 160 57 61 4 472.55 4.21 161 58 61 3 477.20 4.53 162 58 62 4 468.36 2.10 163 59 62 3 477.07 1.94 164 59 63 4 468.42 2.08 165 60 63 3 483.40 2.73 166 60 64 4 468.58 2.02 167 61 64 3 476.14 1.76 168 61 65 4 476.89 2.14 169 62 65 3 486.93 1.49 170 62 66 4 481.09 0.04 171 62 101 39 157.41 1.20 172 63 66 3 481.09 0.04 173 63 67 4 470.81 0.91 174 64 67 3 481.56 0.21 175 64 68 4 470.76 0.89 176 65 68 3 477.57 2.52 177 65 69 4 471.78 1.39 178 65 80 15 157.38 1.30 179 65 83 18 157.34 1.28 180 66 69 3 471.79 1.39 181 66 70 4 473.56 0.50 182 66 105 39 160.60 1.01 183 66 129 63 159.31 0.58 184 66 132 66 157.86 1.30 185 67 70 3 473.56 0.50 186 67 71 4 473.56 0.50 187 68 71 3 474.43 0.94 188 68 72 4 476.39 0.92 189 68 79 11 236.66 2.60 190 68 80 12 236.68 2.60 191 69 72 3 476.41 0.91 192 69 73 4 473.52 0.49 193 69 76 7 284.31 2.40 194 69 80 11 230.19 5.85 195 69 128 59 197.22 2.17 196 69 132 63 159.22 0.83 197 70 73 3 477.67 2.54 198 70 128 58 203.85 1.90 199 72 75 3 471.59 0.30 200 72 76 4 458.44 4.51 201 72 79 7 302.04 5.72 202 73 76 3 478.26 2.23 203 75 78 3 488.38 1.82 204 75 79 4 469.73 3.84 205 76 79 3 477.76 1.74 206 76 80 4 469.73 3.84 207 76 128 52 212.47 0.69 208 76 131 55 212.25 0.72 209 76 132 56 210.99 0.12 210 76 135 59 210.78 0.03 211 77 80 3 487.43 1.40 212 77 81 4 462.25 0.09 213 77 135 58 210.78 0.04 214 78 81 3 484.80 2.71 215 80 83 3 481.75 1.62 216 80 84 4 460.30 1.08 217 80 132 52 212.83 0.86 218 80 135 55 212.68 0.89 219 80 136 56 212.69 0.89 220 81 84 3 467.23 3.35 221 81 85 4 464.94 2.32 222 81 139 58 212.66 0.88 223 82 85 3 473.81 0.43 224 82 86 4 472.13 1.27 225 83 86 3 472.14 1.28 226 83 87 4 472.13 1.28 227 83 136 53 212.80 0.88 228 84 87 3 485.50 3.43 229 84 88 4 472.14 1.28 230 84 135 51 212.94 0.92 231 84 136 52 212.75 0.90 232 84 139 55 212.74 0.90 233 85 88 3 479.89 0.62 234 85 89 4 468.11 0.73 235 85 139 54 212.71 0.88 236 86 89 3 484.81 0.01 237 86 90 4 472.63 3.00 238 86 91 5 441.85 12.38 239 87 91 4 430.41 6.67 240 87 92 5 404.42 6.30 241 87 93 6 404.42 6.30 242 87 98 11 284.67 1.38 243 87 136 49 212.99 0.92 244 87 140 53 212.72 0.91 245 88 92 4 430.41 6.67 246 88 139 51 212.80 0.88 247 88 140 52 212.69 0.90 248 89 92 3 490.07 2.58 249 92 140 48 212.97 0.92 250 93 97 4 478.22 0.20 251 93 98 5 476.60 1.02 252 93 140 47 213.05 0.89 253 94 97 3 498.10 0.20 254 95 98 3 493.29 0.72 255 95 137 42 213.83 0.66 256 95 140 45 213.81 0.66 257 96 99 3 497.29 1.27 258 96 100 4 489.24 2.64 259 97 100 3 485.37 0.57 260 97 101 4 481.31 1.32 261 98 101 3 481.45 1.39 262 98 102 4 477.20 0.19 263 98 133 35 214.47 0.86 264 98 136 38 214.47 0.85 265 98 137 39 214.47 0.86 266 98 140 42 214.46 0.85 267 99 102 3 477.09 0.12 268 99 103 4 472.72 2.06 269 100 103 3 487.17 1.62 270 100 104 4 479.68 0.58 271 101 104 3 485.66 2.38 272 101 105 4 479.69 0.58 273 102 105 3 486.26 2.08 274 102 106 4 479.68 0.58 275 102 129 27 214.79 0.85 276 102 133 31 214.72 0.82 277 103 106 3 487.15 1.63 278 103 107 4 479.68 0.58 279 104 107 3 481.37 4.52 280 104 108 4 465.20 4.31 281 105 108 3 468.92 2.46 282 105 109 4 465.20 4.32 283 105 129 24 215.94 0.54 284 106 109 3 479.30 1.34 285 106 110 4 465.17 4.33 286 106 117 11 219.70 1.42 287 106 122 16 216.27 0.61 288 106 125 19 216.24 0.62 289 106 126 20 216.19 0.61 290 106 129 23 216.16 0.62 291 107 110 3 479.11 0.21 292 107 111 4 463.20 2.31 293 108 111 3 475.93 1.06 294 108 112 4 468.70 0.44 295 109 112 3 478.38 0.16 296 109 113 4 454.89 6.46 297 109 125 16 216.40 0.61 298 110 117 7 220.19 1.64 299 113 116 3 476.85 0.82 300 113 117 4 386.99 6.52 301 115 118 3 515.00 0.95 302 116 121 5 442.75 5.19 303 117 121 4 464.06 5.46 304 117 122 5 441.14 5.95 305 117 125 8 426.62 1.20 306 118 121 3 475.67 4.04 307 118 122 4 462.35 0.55 308 119 122 3 469.69 1.05 309 119 123 4 469.53 1.16 310 120 123 3 487.65 2.56 311 120 124 4 472.85 0.06 312 121 124 3 478.60 2.93 313 121 125 4 472.85 0.06 314 122 125 3 483.67 5.46 315 122 126 4 472.44 0.28 316 123 126 3 481.76 0.92 317 123 127 4 472.43 0.29 318 124 127 3 482.03 1.05 319 124 128 4 469.94 1.53 320 125 128 3 478.56 2.79 321 125 129 4 468.16 0.66 322 126 129 3 479.34 0.29 323 126 130 4 469.64 0.08 324 127 130 3 475.04 2.54 325 127 131 4 472.80 1.43 326 128 131 3 472.74 1.47 327 128 132 4 467.68 4.00 328 129 132 3 476.67 0.82 329 129 133 4 467.68 4.00 330 130 133 3 472.75 5.78 331 130 134 4 473.49 4.69 332 131 134 3 473.49 4.68 333 131 135 4 475.30 3.78 334 132 135 3 479.69 1.58 335 132 136 4 475.31 3.78 336 133 136 3 482.37 0.24 337 133 137 4 482.37 0.24 338 134 137 3 486.14 1.64 339 134 138 4 458.31 0.56 340 135 138 3 476.33 1.85 341 136 140 4 494.35 1.24 342 137 140 3 483.62 4.17