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 5 465.44 3.79 2 2 73 71 31.38 0.18 3 2 127 125 22.05 0.76 4 2 128 126 21.90 0.83 5 2 131 129 21.29 0.58 6 3 6 3 477.00 1.50 7 3 7 4 474.28 2.87 8 4 7 3 474.29 2.87 9 4 8 4 474.39 2.81 10 5 8 3 475.54 3.38 11 5 9 4 471.09 1.14 12 6 9 3 474.89 1.14 13 6 10 4 471.10 1.14 14 6 124 118 46.41 0.13 15 6 127 121 46.40 0.12 16 7 10 3 476.65 3.91 17 7 11 4 471.10 1.14 18 7 73 66 47.85 0.13 19 7 74 67 47.91 0.16 20 8 11 3 477.54 1.28 21 8 12 4 471.09 1.15 22 9 12 3 476.35 0.68 23 9 13 4 467.06 2.69 24 9 121 112 62.71 0.05 25 9 124 115 62.52 0.04 26 10 13 3 474.75 0.39 27 10 14 4 471.19 1.47 28 10 70 60 62.48 0.01 29 10 124 114 62.66 0.03 30 10 125 115 62.53 0.04 31 10 128 118 62.51 0.04 32 11 14 3 477.06 1.54 33 11 15 4 474.16 2.96 34 11 70 59 62.54 0.01 35 11 71 60 62.69 0.04 36 11 73 62 62.70 0.04 37 12 15 3 477.08 1.56 38 12 16 4 474.23 2.96 39 13 16 3 478.25 1.22 40 13 17 4 477.90 1.13 41 13 113 100 75.06 1.15 42 13 121 108 62.91 0.10 43 13 125 112 62.80 0.05 44 14 17 3 477.04 1.54 45 14 18 4 474.20 2.96 46 14 21 7 408.53 3.85 47 14 66 52 62.79 0.04 48 14 67 53 62.79 0.04 49 14 70 56 62.80 0.04 50 14 109 95 74.94 1.19 51 15 18 3 477.74 0.96 52 16 113 97 80.71 3.90 53 16 116 100 75.38 1.29 54 17 20 3 489.57 2.64 55 17 21 4 448.56 3.06 56 17 24 7 414.69 7.17 57 17 109 92 75.36 1.30 58 17 113 96 81.16 3.70 59 18 21 3 503.33 1.19 60 20 23 3 478.01 1.17 61 20 24 4 465.79 3.37 62 21 24 3 480.74 2.58 63 21 25 4 468.01 2.25 64 21 63 42 89.22 0.09 65 22 25 3 473.19 0.33 66 22 26 4 468.05 2.26 67 22 60 38 93.09 1.79 68 22 63 41 93.06 1.78 69 23 26 3 474.95 0.11 70 23 27 4 468.06 2.26 71 24 27 3 469.36 2.91 72 24 28 4 468.06 2.26 73 24 108 84 120.00 0.82 74 24 109 85 122.91 0.64 75 24 112 88 128.25 0.85 76 25 28 3 471.90 1.64 77 25 29 4 466.20 3.18 78 25 59 34 115.40 0.45 79 26 29 3 477.88 0.13 80 26 30 4 462.06 1.11 81 26 55 29 120.28 0.14 82 26 56 30 120.82 0.17 83 26 59 33 116.59 0.85 84 27 30 3 469.77 3.93 85 27 31 4 461.99 1.14 86 27 108 81 128.75 0.88 87 27 112 85 129.11 0.79 88 28 31 3 469.19 2.81 89 28 32 4 465.82 3.06 90 28 104 76 128.66 0.89 91 28 105 77 128.69 0.86 92 28 108 80 128.76 0.88 93 29 32 3 468.55 1.70 94 29 33 4 464.70 0.26 95 29 55 26 128.96 0.79 96 29 58 29 128.92 0.81 97 29 59 30 128.76 0.89 98 29 101 72 128.70 0.87 99 30 33 3 478.72 0.61 100 30 34 4 467.37 1.06 101 30 50 20 129.59 0.90 102 31 34 3 479.83 1.16 103 31 35 4 467.36 1.06 104 31 104 73 128.87 0.96 105 31 107 76 129.46 0.90 106 31 108 77 129.46 0.90 107 32 35 3 468.93 1.85 108 32 36 4 449.49 1.84 109 32 39 7 301.01 5.76 110 32 101 69 128.87 0.96 111 32 104 72 129.07 0.88 112 33 37 4 440.31 1.80 113 33 39 6 307.56 9.04 114 33 40 7 227.40 27.62 115 33 43 10 237.33 37.61 116 33 48 15 129.64 0.89 117 34 37 3 487.19 0.17 118 36 39 3 492.82 0.10 119 36 100 64 128.88 0.96 120 36 103 67 129.59 0.94 121 36 104 68 129.54 0.92 122 37 40 3 488.63 1.03 123 38 41 3 487.75 1.47 124 39 42 3 496.04 1.72 125 39 43 4 488.26 0.74 126 39 97 58 128.93 1.03 127 39 100 61 129.56 0.96 128 40 43 3 488.26 0.74 129 40 44 4 487.10 1.32 130 40 48 8 143.62 4.72 131 41 44 3 497.29 1.07 132 42 93 51 129.00 0.99 133 42 94 52 129.17 0.99 134 42 97 55 129.45 1.05 135 43 46 3 481.94 0.27 136 43 48 5 368.36 18.18 137 43 58 15 129.96 1.01 138 45 54 9 133.73 0.24 139 46 54 8 133.73 0.25 140 46 55 9 133.72 0.25 141 46 58 12 133.72 0.26 142 47 52 5 220.22 33.89 143 47 54 7 133.76 0.23 144 47 55 8 133.81 0.21 145 48 55 7 208.12 36.95 146 49 52 3 467.74 6.67 147 51 56 5 451.63 1.79 148 52 55 3 474.44 0.45 149 52 56 4 461.48 3.11 150 53 56 3 478.27 3.29 151 53 57 4 461.49 3.12 152 54 57 3 474.19 0.33 153 54 58 4 461.49 3.12 154 55 58 3 475.78 2.04 155 55 59 4 459.47 0.96 156 56 59 3 473.36 0.74 157 56 60 4 469.81 2.52 158 57 60 3 474.30 1.27 159 57 61 4 469.81 2.52 160 58 61 3 474.50 0.17 161 58 62 4 465.05 0.09 162 59 62 3 480.49 2.83 163 59 63 4 465.16 0.14 164 60 63 3 469.47 1.49 165 60 64 4 465.16 0.14 166 61 64 3 479.20 3.48 167 61 65 4 467.55 1.33 168 62 65 3 475.53 5.32 169 62 66 4 468.67 1.90 170 63 66 3 478.32 2.93 171 63 67 4 466.84 0.62 172 64 67 3 477.16 3.51 173 64 68 4 466.89 0.60 174 65 68 3 477.41 3.34 175 65 69 4 474.90 4.60 176 65 80 15 153.67 2.37 177 65 83 18 143.78 2.50 178 66 69 3 476.50 3.81 179 66 70 4 466.91 0.61 180 66 105 39 161.47 1.28 181 66 129 63 154.85 1.80 182 66 132 66 153.78 2.33 183 67 70 3 475.75 4.18 184 67 71 4 466.89 0.61 185 68 71 3 472.69 2.65 186 68 72 4 466.87 0.62 187 68 79 11 170.11 4.41 188 68 80 12 161.14 1.06 189 69 72 3 477.42 1.74 190 69 73 4 460.30 2.66 191 69 76 7 282.90 4.03 192 69 80 11 153.79 2.42 193 69 128 59 189.10 4.17 194 69 132 63 156.15 1.29 195 70 73 3 464.37 0.64 196 70 128 58 211.96 4.70 197 72 75 3 470.84 0.01 198 72 76 4 430.68 6.36 199 72 79 7 283.53 3.83 200 73 76 3 473.44 0.39 201 75 78 3 495.31 0.51 202 75 79 4 454.81 3.56 203 76 79 3 468.52 3.29 204 76 80 4 452.55 1.72 205 76 128 52 273.53 1.28 206 76 131 55 273.38 1.25 207 76 132 56 272.65 1.61 208 76 135 59 272.64 1.61 209 77 80 3 486.94 1.12 210 77 81 4 461.66 6.28 211 77 135 58 272.64 1.61 212 78 81 3 470.84 4.45 213 80 83 3 479.81 2.52 214 80 84 4 458.61 6.10 215 80 132 52 274.95 0.81 216 80 135 55 274.88 0.83 217 80 136 56 274.88 0.83 218 81 84 3 468.79 2.99 219 81 85 4 466.41 2.21 220 81 139 58 274.89 0.83 221 82 85 3 480.70 1.72 222 82 86 4 467.16 1.82 223 83 86 3 474.86 2.05 224 83 87 4 467.15 1.81 225 83 136 53 275.11 0.89 226 84 87 3 480.84 0.92 227 84 88 4 467.16 1.80 228 84 135 51 275.22 0.89 229 84 136 52 275.08 0.89 230 84 138 54 275.05 0.89 231 84 139 55 275.00 0.89 232 85 88 3 474.81 2.07 233 85 89 4 456.49 7.14 234 85 90 5 449.54 3.66 235 85 139 54 275.03 0.90 236 86 90 4 426.95 6.35 237 86 91 5 390.53 4.64 238 87 91 4 369.88 7.33 239 87 92 5 355.60 14.46 240 87 93 6 347.98 10.66 241 87 98 11 290.16 6.89 242 87 136 49 275.23 0.89 243 87 140 53 275.00 0.89 244 88 92 4 359.27 5.01 245 88 139 51 275.06 0.90 246 88 140 52 275.00 0.89 247 89 92 3 483.11 0.58 248 89 139 50 275.13 0.86 249 93 97 4 480.54 0.75 250 93 98 5 473.86 1.74 251 93 140 47 275.32 0.85 252 94 97 3 494.81 0.05 253 95 98 3 494.81 0.05 254 95 137 42 275.69 0.92 255 95 140 45 275.61 0.91 256 96 99 3 493.31 0.38 257 96 100 4 482.78 0.36 258 97 100 3 478.17 0.44 259 97 101 4 480.56 3.85 260 98 101 3 480.55 3.85 261 98 102 4 471.25 2.38 262 98 133 35 275.99 0.97 263 98 136 38 276.04 0.96 264 98 137 39 275.98 0.98 265 98 140 42 275.98 0.98 266 99 102 3 477.38 5.44 267 99 103 4 471.25 2.38 268 100 103 3 482.68 2.79 269 100 104 4 478.45 4.91 270 101 104 3 482.68 2.80 271 101 105 4 475.98 3.67 272 102 105 3 475.99 3.67 273 102 106 4 476.69 3.31 274 102 129 27 276.33 0.99 275 102 133 31 276.28 0.96 276 103 106 3 467.39 1.63 277 103 107 4 466.44 1.82 278 104 107 3 482.70 2.80 279 104 108 4 468.94 4.08 280 105 108 3 482.73 2.79 281 105 109 4 468.96 4.09 282 105 129 24 276.56 1.07 283 106 109 3 483.36 3.10 284 106 110 4 468.97 4.10 285 106 117 11 277.91 1.28 286 106 122 16 277.23 1.12 287 106 125 19 276.98 1.22 288 106 126 20 276.92 1.24 289 106 129 23 276.91 1.24 290 107 110 3 474.17 1.50 291 107 111 4 472.43 2.37 292 108 111 3 484.86 0.71 293 108 112 4 460.63 0.05 294 109 112 3 480.28 1.54 295 109 113 4 450.61 0.84 296 109 125 16 277.25 1.32 297 110 113 3 477.75 2.81 298 110 117 7 277.78 1.36 299 113 116 3 466.70 4.27 300 113 117 4 367.51 16.11 301 116 121 5 465.65 2.83 302 117 121 4 465.66 2.83 303 117 122 5 448.19 5.66 304 117 125 8 421.81 11.41 305 118 121 3 467.40 1.96 306 118 122 4 475.34 2.01 307 119 122 3 475.35 2.01 308 119 123 4 475.35 2.01 309 120 123 3 475.37 2.02 310 120 124 4 475.35 2.01 311 121 124 3 475.36 2.02 312 121 125 4 475.33 2.02 313 122 125 3 474.57 2.41 314 122 126 4 472.68 3.35 315 123 126 3 478.27 0.56 316 123 127 4 472.73 3.33 317 124 127 3 472.92 3.18 318 124 128 4 471.37 2.65 319 125 128 3 483.64 3.16 320 125 129 4 471.37 2.66 321 126 129 3 490.55 0.29 322 126 130 4 471.31 2.41 323 127 130 3 480.26 4.84 324 127 131 4 472.28 1.94 325 128 131 3 474.75 2.09 326 128 132 4 472.30 1.95 327 129 132 3 473.62 1.52 328 129 133 4 472.32 1.96 329 130 133 3 472.33 1.96 330 130 134 4 472.32 1.96 331 131 134 3 472.30 1.98 332 131 135 4 472.29 1.98 333 132 135 3 473.50 1.49 334 132 136 4 468.94 3.65 335 133 136 3 470.10 3.23 336 133 137 4 462.19 0.28 337 134 137 3 477.38 0.79 338 134 138 4 464.38 1.22 339 135 138 3 477.00 0.01 340 136 140 4 495.74 2.69 341 137 140 3 486.87 0.07