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 6 4 474.19 2.90 2 2 7 5 454.87 1.38 3 2 10 8 438.56 3.70 4 2 73 71 32.38 0.65 5 2 127 125 27.62 1.50 6 2 128 126 24.25 0.18 7 2 131 129 22.43 0.73 8 3 6 3 477.02 1.51 9 3 7 4 477.00 1.50 10 4 7 3 492.54 3.58 11 4 8 4 474.39 2.81 12 5 8 3 477.01 1.51 13 5 9 4 470.96 1.09 14 6 9 3 471.04 1.13 15 6 10 4 471.04 1.14 16 6 124 118 48.27 0.96 17 6 127 121 47.80 1.19 18 7 10 3 474.55 0.29 19 7 11 4 465.55 3.90 20 7 73 66 50.58 1.59 21 7 74 67 50.58 1.59 22 8 11 3 479.91 0.09 23 8 12 4 465.56 3.91 24 9 12 3 475.94 0.89 25 9 13 4 461.81 5.79 26 9 120 111 54.81 2.60 27 9 121 112 54.66 2.62 28 9 124 115 54.59 2.65 29 10 13 3 474.04 3.08 30 10 14 4 459.76 6.82 31 10 70 60 54.59 2.65 32 10 124 114 54.64 2.64 33 10 125 115 54.61 2.65 34 10 128 118 54.58 2.64 35 11 15 4 462.94 5.21 36 11 70 59 54.59 2.65 37 11 73 62 54.60 2.65 38 12 15 3 474.50 0.57 39 12 16 4 463.39 4.98 40 13 16 3 474.44 0.60 41 13 17 4 463.43 4.99 42 13 113 100 71.47 1.19 43 13 121 108 55.34 2.85 44 13 125 112 55.30 2.83 45 14 17 3 463.44 4.99 46 14 18 4 463.43 5.00 47 14 21 7 406.23 11.44 48 14 66 52 56.98 2.02 49 14 67 53 56.98 2.02 50 14 70 56 55.34 2.84 51 14 109 95 71.52 1.21 52 15 18 3 474.65 0.58 53 16 113 97 92.51 1.51 54 16 116 100 87.25 4.12 55 17 20 3 489.19 2.83 56 17 21 4 440.87 1.52 57 17 24 7 393.56 1.44 58 17 109 92 87.24 4.12 59 17 113 96 98.11 1.28 60 18 21 3 502.39 0.72 61 20 23 3 477.96 1.20 62 20 24 4 468.07 2.27 63 21 24 3 474.09 0.74 64 21 25 4 468.10 2.25 65 21 63 42 102.94 1.44 66 22 25 3 469.72 1.44 67 22 26 4 469.70 1.44 68 22 59 37 113.45 0.27 69 22 60 38 106.91 0.52 70 22 63 41 106.89 0.54 71 23 26 3 478.16 2.79 72 23 27 4 471.15 2.16 73 24 27 3 479.61 2.06 74 24 28 4 466.67 1.53 75 24 108 84 128.13 1.24 76 24 109 85 128.18 2.00 77 24 112 88 136.06 0.08 78 25 28 3 480.80 2.66 79 25 29 4 463.61 2.17 80 25 59 34 120.70 0.47 81 25 63 38 120.44 0.54 82 26 29 3 480.68 1.27 83 26 30 4 461.37 1.45 84 26 55 29 134.96 0.42 85 26 56 30 134.65 0.42 86 26 59 33 120.87 0.41 87 27 30 3 463.74 2.23 88 27 31 4 461.58 1.34 89 27 108 81 136.35 0.15 90 27 112 85 136.44 0.14 91 28 31 3 469.33 5.03 92 28 32 4 463.55 2.33 93 28 101 73 136.18 0.10 94 28 104 76 136.23 0.11 95 28 105 77 136.24 0.10 96 28 108 80 136.38 0.14 97 29 32 3 464.21 2.64 98 29 33 4 461.50 1.28 99 29 55 26 136.52 0.18 100 29 58 29 136.41 0.16 101 29 59 30 136.36 0.14 102 29 62 33 136.37 0.14 103 29 101 72 136.28 0.10 104 30 33 3 472.59 3.68 105 30 34 4 463.10 2.08 106 30 50 20 136.92 0.28 107 31 34 3 478.73 0.61 108 31 35 4 463.29 2.18 109 31 104 73 136.55 0.17 110 31 107 76 136.67 0.20 111 31 108 77 136.70 0.18 112 31 111 80 136.97 0.25 113 32 35 3 479.67 1.79 114 32 36 4 463.27 2.19 115 32 39 7 344.41 15.95 116 32 100 68 136.52 0.15 117 32 101 69 136.50 0.15 118 32 104 72 136.60 0.17 119 33 36 3 481.58 4.61 120 33 37 4 443.78 0.17 121 33 39 6 343.44 15.46 122 33 40 7 303.82 1.56 123 33 43 10 289.14 5.79 124 33 48 15 136.96 0.29 125 33 55 22 136.95 0.27 126 34 37 3 486.79 3.08 127 36 39 3 494.29 0.64 128 36 100 64 136.60 0.16 129 36 104 68 136.94 0.25 130 37 40 3 486.96 1.86 131 38 41 3 496.97 2.19 132 39 42 3 496.04 1.73 133 39 43 4 487.68 1.03 134 39 97 58 136.53 0.18 135 39 100 61 136.93 0.25 136 40 43 3 487.07 1.33 137 40 48 8 224.23 0.06 138 41 44 3 483.49 1.06 139 42 93 51 136.41 0.15 140 42 94 52 136.90 0.24 141 42 97 55 136.94 0.25 142 43 46 3 479.92 2.25 143 43 48 5 422.07 7.86 144 43 58 15 137.40 0.22 145 46 54 8 229.53 2.19 146 46 58 12 229.39 2.13 147 47 52 5 238.83 2.70 148 47 54 7 229.54 2.19 149 47 55 8 229.55 2.19 150 48 55 7 229.53 2.18 151 49 52 3 476.61 3.52 152 52 55 3 485.41 0.29 153 52 56 4 478.38 3.23 154 53 56 3 478.39 3.23 155 53 57 4 465.80 3.06 156 54 57 3 474.46 0.46 157 54 58 4 465.88 3.10 158 55 58 3 468.81 1.65 159 55 59 4 473.31 0.61 160 56 59 3 473.32 0.61 161 56 60 4 473.34 0.60 162 57 60 3 474.49 1.17 163 57 61 4 473.35 0.60 164 58 61 3 473.48 0.67 165 58 62 4 473.36 0.61 166 59 62 3 480.37 2.89 167 59 63 4 472.42 1.08 168 60 63 3 472.46 1.07 169 60 64 4 472.40 1.09 170 61 64 3 480.38 2.89 171 61 65 4 472.69 0.96 172 62 65 3 473.54 0.53 173 62 66 4 472.69 0.96 174 62 101 39 153.68 2.59 175 63 66 3 477.49 3.35 176 63 67 4 464.44 3.18 177 64 67 3 477.49 3.35 178 64 68 4 474.65 4.63 179 65 68 3 477.43 3.33 180 65 69 4 474.31 4.90 181 65 83 18 165.21 3.43 182 66 69 3 476.50 3.81 183 66 70 4 474.31 4.90 184 66 105 39 169.85 1.22 185 66 128 62 172.15 0.27 186 66 129 63 169.76 1.26 187 66 132 66 168.25 2.00 188 67 70 3 475.75 4.18 189 67 71 4 474.31 4.90 190 68 71 3 479.44 0.66 191 68 72 4 463.97 7.08 192 68 79 11 230.35 2.46 193 69 72 3 469.76 4.19 194 69 73 4 451.51 0.85 195 69 76 7 270.31 5.64 196 69 80 11 219.49 4.26 197 69 128 59 175.91 2.12 198 69 132 63 169.83 1.35 199 70 73 3 461.93 3.48 200 70 128 58 179.60 0.39 201 72 75 3 481.50 3.83 202 72 76 4 413.39 6.29 203 72 79 7 275.32 0.18 204 73 76 3 483.65 2.76 205 75 78 3 495.31 0.51 206 75 79 4 462.01 0.05 207 76 79 3 462.02 0.04 208 76 80 4 436.97 5.38 209 76 128 52 203.00 1.22 210 76 131 55 202.56 1.43 211 76 132 56 202.41 1.50 212 76 135 59 200.47 0.55 213 77 81 4 436.97 5.38 214 77 135 58 202.40 1.51 215 77 140 63 189.37 3.58 216 78 81 3 468.47 0.16 217 80 83 3 489.09 2.43 218 80 84 4 474.01 0.39 219 80 132 52 203.88 1.05 220 80 135 55 203.44 1.06 221 80 136 56 203.50 1.10 222 81 84 3 486.11 1.54 223 81 85 4 474.53 0.66 224 82 85 3 495.04 6.02 225 82 86 4 474.53 0.66 226 83 86 3 479.26 1.72 227 83 87 4 472.08 0.54 228 83 136 53 203.88 1.03 229 84 87 3 479.26 1.72 230 84 88 4 472.03 0.51 231 84 89 5 467.37 1.77 232 84 135 51 203.88 1.03 233 84 136 52 203.88 1.03 234 84 138 54 203.87 1.03 235 85 88 3 476.86 2.92 236 85 89 4 462.94 0.39 237 85 90 5 440.84 2.08 238 86 90 4 440.62 1.97 239 86 91 5 435.71 4.42 240 87 91 4 435.64 4.40 241 87 92 5 427.79 8.29 242 87 93 6 360.84 14.36 243 87 98 11 271.33 2.98 244 87 136 49 203.98 1.05 245 88 92 4 400.36 5.40 246 88 136 48 204.03 1.07 247 88 137 49 203.92 1.03 248 88 138 50 203.92 1.03 249 88 139 51 203.84 1.04 250 89 92 3 478.56 1.69 251 89 139 50 203.82 1.03 252 92 139 47 204.00 1.05 253 93 97 4 476.81 0.25 254 93 98 5 466.47 1.96 255 94 97 3 489.19 2.85 256 95 98 3 494.81 0.05 257 95 137 42 204.33 0.98 258 96 99 3 494.49 0.21 259 96 100 4 482.75 0.35 260 97 100 3 486.98 3.97 261 97 101 4 474.78 2.13 262 98 101 3 473.86 2.59 263 98 102 4 464.02 1.43 264 98 133 35 205.17 0.99 265 98 136 38 205.18 0.99 266 98 137 39 205.13 1.01 267 99 102 3 471.44 2.27 268 99 103 4 471.44 2.27 269 100 103 3 474.42 0.80 270 100 104 4 471.43 2.29 271 101 104 3 473.34 1.33 272 101 105 4 475.98 3.67 273 102 105 3 476.99 3.17 274 102 106 4 475.98 3.67 275 102 129 27 205.50 0.94 276 102 133 31 205.31 0.96 277 103 106 3 476.99 3.17 278 103 107 4 475.99 3.67 279 104 107 3 482.67 2.80 280 104 108 4 476.69 3.31 281 105 108 3 469.98 3.56 282 105 109 4 466.35 1.85 283 105 129 24 206.94 0.54 284 106 109 3 479.81 4.87 285 106 110 4 476.72 3.33 286 106 117 11 211.90 2.29 287 106 122 16 207.31 0.53 288 106 125 19 207.30 0.53 289 106 126 20 207.06 0.57 290 106 129 23 207.12 0.59 291 107 110 3 480.29 1.58 292 107 111 4 477.27 3.06 293 108 111 3 487.92 0.82 294 108 112 4 472.25 5.57 295 109 112 3 480.12 1.62 296 109 113 4 458.91 6.16 297 109 125 16 207.80 0.56 298 110 113 3 480.25 1.55 299 110 117 7 247.75 1.74 300 113 116 3 481.39 2.14 301 113 117 4 416.27 11.92 302 115 118 3 514.82 4.83 303 116 121 5 459.44 0.62 304 117 121 4 459.47 0.64 305 117 122 5 459.41 0.65 306 117 125 8 404.66 5.81 307 118 121 3 468.54 1.09 308 118 122 4 461.44 0.26 309 119 122 3 479.93 4.36 310 119 123 4 464.40 0.45 311 120 123 3 472.93 0.86 312 120 124 4 473.42 1.48 313 121 124 3 473.42 1.48 314 121 125 4 470.84 2.77 315 122 125 3 473.36 1.80 316 122 126 4 471.25 2.57 317 123 126 3 476.87 0.10 318 123 127 4 471.25 2.57 319 124 127 3 477.00 0.17 320 124 128 4 471.20 2.54 321 125 128 3 479.14 1.24 322 125 129 4 471.19 2.53 323 126 129 3 484.11 0.28 324 126 130 4 472.69 3.29 325 127 130 3 481.96 1.35 326 127 131 4 471.05 2.51 327 128 131 3 478.35 0.29 328 128 132 4 463.68 0.70 329 129 132 3 477.21 0.28 330 129 133 4 464.93 1.32 331 130 133 3 464.94 1.31 332 130 134 4 464.93 1.32 333 131 134 3 473.59 1.53 334 131 135 4 468.31 1.09 335 132 135 3 489.37 2.36 336 132 136 4 468.32 1.10 337 133 136 3 474.32 1.26 338 133 137 4 473.68 1.57 339 134 137 3 477.97 0.49 340 134 138 4 476.32 0.26 341 135 138 3 472.60 2.19