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 5 455.56 4.52 2 2 73 71 30.12 0.41 3 2 76 74 26.46 0.61 4 2 127 125 22.82 0.30 5 2 128 126 22.25 0.15 6 2 131 129 21.99 0.04 7 3 6 3 475.94 0.52 8 3 7 4 469.21 2.27 9 4 7 3 473.31 0.23 10 4 8 4 474.41 0.33 11 5 8 3 476.95 1.59 12 5 9 4 474.44 0.35 13 6 9 3 477.72 1.21 14 6 10 4 469.20 2.96 15 6 124 118 45.92 0.14 16 6 127 121 45.62 0.30 17 7 10 3 476.82 1.66 18 7 11 4 469.20 2.94 19 7 73 66 47.79 1.08 20 7 74 67 50.70 0.35 21 8 11 3 474.69 0.21 22 8 12 4 469.20 2.95 23 9 12 3 477.05 0.10 24 9 13 4 469.15 2.93 25 9 121 112 59.72 0.01 26 9 124 115 59.70 0.01 27 10 13 3 477.94 1.49 28 10 14 4 469.10 2.92 29 10 70 60 59.73 0.06 30 10 124 114 59.73 0.02 31 10 125 115 59.69 0.03 32 10 128 118 59.65 0.01 33 11 15 4 448.22 2.75 34 11 70 59 59.76 0.07 35 11 71 60 59.77 0.07 36 11 73 62 59.76 0.07 37 12 15 3 461.72 5.74 38 12 16 4 469.54 1.81 39 13 16 3 477.82 1.42 40 13 17 4 465.04 0.45 41 13 113 100 70.81 0.32 42 13 121 108 60.35 0.14 43 13 125 112 60.12 0.04 44 14 17 3 466.62 1.25 45 14 18 4 465.03 0.46 46 14 66 52 60.10 0.04 47 14 67 53 60.09 0.03 48 14 70 56 60.11 0.04 49 14 109 95 70.80 0.31 50 15 18 3 472.01 1.44 51 16 116 100 91.14 2.10 52 17 20 3 484.95 0.69 53 17 21 4 429.39 6.53 54 17 24 7 393.12 14.06 55 17 109 92 85.67 1.83 56 17 113 96 91.16 2.10 57 18 21 3 488.34 2.88 58 20 23 3 474.04 0.76 59 20 24 4 465.93 1.68 60 21 24 3 469.07 0.12 61 21 25 4 465.92 1.68 62 21 63 42 98.21 1.46 63 22 25 3 469.06 0.12 64 22 26 4 464.41 2.44 65 22 60 38 102.52 1.49 66 22 63 41 98.27 1.44 67 23 26 3 480.26 5.50 68 23 27 4 464.26 2.49 69 23 56 33 117.97 0.17 70 24 27 3 481.81 4.73 71 24 28 4 461.70 1.21 72 24 108 84 121.92 1.61 73 24 109 85 126.57 0.42 74 24 112 88 129.47 0.50 75 24 113 89 129.61 0.45 76 25 28 3 468.31 1.92 77 25 29 4 468.63 2.87 78 25 59 34 117.97 0.17 79 26 29 3 469.58 0.94 80 26 30 4 463.85 0.12 81 26 55 29 126.51 0.66 82 26 56 30 124.92 1.26 83 26 59 33 120.33 1.03 84 27 30 3 464.06 0.71 85 27 31 4 463.65 0.38 86 27 108 81 129.65 0.45 87 27 112 85 130.75 0.83 88 28 31 3 468.89 1.79 89 28 32 4 463.66 0.38 90 28 101 73 129.53 0.48 91 28 104 76 129.56 0.48 92 28 105 77 129.53 0.48 93 28 108 80 129.73 0.48 94 29 32 3 468.96 0.12 95 29 33 4 464.63 1.55 96 29 55 26 130.30 0.60 97 29 58 29 130.28 0.61 98 29 59 30 129.85 0.53 99 29 62 33 129.80 0.56 100 29 101 72 129.56 0.49 101 30 33 3 484.35 1.05 102 30 34 4 462.99 0.72 103 30 50 20 130.83 0.83 104 31 34 3 482.74 1.86 105 31 35 4 465.35 1.20 106 31 104 73 130.01 0.70 107 31 107 76 130.62 0.90 108 31 108 77 130.74 0.83 109 32 35 3 473.97 0.67 110 32 36 4 461.68 1.38 111 32 39 7 307.38 2.90 112 32 100 68 130.00 0.70 113 32 101 69 129.99 0.70 114 32 104 72 130.57 0.89 115 33 37 4 422.77 2.46 116 33 39 6 234.82 26.11 117 33 40 7 212.39 26.22 118 33 43 10 204.68 22.37 119 33 48 15 130.88 0.82 120 36 39 3 488.83 2.33 121 36 100 64 130.00 0.70 122 36 103 67 130.76 0.84 123 36 104 68 130.77 0.85 124 37 40 3 482.18 1.00 125 38 41 3 487.44 1.62 126 39 42 3 487.84 1.41 127 39 43 4 483.15 0.64 128 39 97 58 129.97 0.69 129 39 100 61 130.72 0.83 130 40 43 3 489.88 4.00 131 40 48 8 134.81 0.65 132 41 44 3 494.28 1.80 133 42 93 51 129.94 0.70 134 42 94 52 130.46 0.94 135 42 97 55 130.63 0.89 136 43 46 3 477.87 1.02 137 43 48 5 411.44 0.58 138 43 58 15 131.06 0.83 139 45 54 9 135.19 0.49 140 46 54 8 135.19 0.49 141 46 58 12 135.14 0.49 142 47 52 5 184.43 3.15 143 47 54 7 135.21 0.48 144 47 55 8 135.21 0.48 145 48 55 7 152.56 8.20 146 49 52 3 480.78 3.28 147 52 55 3 473.57 1.06 148 52 56 4 472.57 1.41 149 53 56 3 474.06 2.15 150 53 57 4 464.13 2.81 151 54 57 3 472.56 1.40 152 54 58 4 464.14 2.82 153 55 58 3 464.15 2.82 154 55 59 4 461.75 4.00 155 56 59 3 472.03 1.12 156 56 60 4 471.15 0.69 157 57 60 3 483.44 4.46 158 57 61 4 471.18 0.70 159 58 61 3 472.62 0.02 160 58 62 4 471.15 0.73 161 59 62 3 479.26 2.79 162 59 63 4 471.16 0.73 163 60 63 3 471.94 1.18 164 60 64 4 471.10 0.76 165 61 64 3 472.03 1.24 166 61 65 4 472.62 0.00 167 62 65 3 483.15 0.40 168 62 66 4 467.38 2.62 169 63 66 3 475.68 1.52 170 63 67 4 467.38 2.62 171 64 67 3 467.20 0.59 172 64 68 4 465.26 1.56 173 65 68 3 467.74 0.86 174 65 69 4 465.26 1.55 175 65 83 18 145.10 0.39 176 66 69 3 465.68 1.34 177 66 70 4 465.23 1.54 178 66 105 39 169.88 3.67 179 66 128 62 183.23 2.90 180 66 129 63 167.15 2.30 181 66 132 66 154.27 1.39 182 67 70 3 471.12 3.43 183 67 71 4 457.88 1.77 184 68 71 3 470.86 3.29 185 68 72 4 457.88 1.77 186 68 79 11 205.84 24.05 187 69 72 3 472.63 2.75 188 69 73 4 439.56 2.98 189 69 76 7 233.11 21.20 190 69 80 11 197.19 19.73 191 69 128 59 217.56 12.08 192 69 132 63 169.66 3.62 193 70 73 3 463.06 4.80 194 70 128 58 212.43 14.66 195 72 75 3 471.42 0.29 196 72 76 4 424.56 12.11 197 72 79 7 279.99 0.17 198 73 76 3 479.46 1.52 199 75 78 3 483.22 0.32 200 75 79 4 469.56 1.56 201 76 79 3 471.73 0.49 202 76 80 4 462.35 1.27 203 76 128 52 249.09 7.71 204 76 131 55 248.75 7.84 205 76 132 56 248.27 8.03 206 77 80 3 485.14 1.28 207 77 81 4 460.88 0.53 208 77 135 58 247.85 8.22 209 78 81 3 472.38 0.18 210 80 83 3 479.43 0.58 211 80 84 4 465.94 1.06 212 80 132 52 249.46 7.77 213 80 135 55 249.09 7.72 214 80 136 56 249.11 7.73 215 81 84 3 478.20 1.19 216 81 85 4 472.82 1.50 217 81 139 58 249.12 7.70 218 82 85 3 485.62 1.86 219 82 86 4 477.42 3.79 220 83 86 3 485.62 1.86 221 83 87 4 477.42 3.79 222 83 136 53 249.56 7.72 223 84 87 3 481.43 1.79 224 84 88 4 474.90 5.05 225 84 135 51 249.58 7.72 226 84 136 52 249.56 7.72 227 84 139 55 249.41 7.72 228 85 88 3 478.64 3.19 229 85 89 4 463.45 0.67 230 85 139 54 249.50 7.73 231 86 89 3 486.92 0.96 232 86 90 4 442.94 0.24 233 86 91 5 435.23 4.09 234 87 91 4 410.97 5.59 235 87 92 5 337.74 15.61 236 87 93 6 316.95 14.08 237 87 98 11 278.18 2.77 238 87 136 49 249.74 7.75 239 87 140 53 249.52 7.74 240 88 92 4 333.60 17.67 241 88 139 51 249.58 7.71 242 88 140 52 249.38 7.71 243 89 92 3 490.06 1.74 244 89 139 50 249.71 7.75 245 92 140 48 249.68 7.73 246 93 97 4 482.23 0.20 247 93 98 5 479.73 1.23 248 93 140 47 249.86 7.79 249 94 97 3 487.45 0.42 250 94 98 4 484.62 0.99 251 95 98 3 484.62 0.99 252 95 140 45 250.10 7.75 253 96 99 3 492.32 5.33 254 96 100 4 481.03 0.57 255 97 100 3 480.03 1.03 256 97 101 4 480.02 1.03 257 98 101 3 477.73 2.42 258 98 102 4 473.29 1.35 259 98 133 35 250.68 7.89 260 98 136 38 250.69 7.89 261 98 137 39 250.66 7.90 262 98 140 42 250.66 7.89 263 99 102 3 474.45 0.78 264 99 103 4 473.30 1.35 265 100 103 3 478.35 0.25 266 100 104 4 473.29 1.35 267 101 104 3 476.09 0.06 268 101 105 4 464.31 1.66 269 102 105 3 473.25 2.80 270 102 106 4 464.31 1.66 271 102 129 27 251.24 7.87 272 102 133 31 251.22 7.87 273 103 106 3 470.07 1.19 274 103 107 4 464.12 1.75 275 104 107 3 470.55 0.28 276 104 108 4 463.43 1.44 277 105 108 3 471.73 2.71 278 105 109 4 468.48 1.09 279 105 129 24 251.97 7.98 280 106 109 3 471.90 2.80 281 106 110 4 461.79 2.25 282 106 117 11 253.31 7.61 283 106 122 16 252.74 7.70 284 106 125 19 252.69 7.71 285 106 126 20 252.69 7.71 286 106 129 23 252.63 7.69 287 107 110 3 474.01 1.43 288 107 111 4 459.65 1.52 289 108 111 3 477.35 3.08 290 108 112 4 465.00 1.15 291 109 112 3 469.23 0.97 292 109 113 4 451.41 5.63 293 109 125 16 253.02 7.55 294 110 117 7 253.34 7.59 295 113 116 3 483.60 0.90 296 113 117 4 459.86 3.96 297 114 117 3 482.03 0.70 298 115 118 3 520.57 1.96 299 116 121 5 451.03 2.73 300 117 121 4 458.85 0.15 301 117 122 5 440.37 8.05 302 117 125 8 424.37 0.25 303 118 121 3 462.94 1.17 304 118 122 4 461.01 0.20 305 119 122 3 467.40 1.05 306 119 123 4 461.05 0.21 307 120 123 3 475.18 1.99 308 120 124 4 461.05 0.21 309 121 124 3 466.38 2.44 310 121 125 4 461.04 0.21 311 122 125 3 474.44 1.99 312 122 126 4 461.00 0.23 313 123 126 3 474.84 1.78 314 123 127 4 460.67 0.07 315 124 127 3 474.82 1.66 316 124 128 4 465.83 0.29 317 125 128 3 474.00 2.71 318 125 129 4 467.89 0.73 319 126 129 3 484.62 0.62 320 126 130 4 468.89 1.24 321 127 130 3 476.49 4.69 322 127 131 4 465.85 0.29 323 128 131 3 476.48 4.69 324 128 132 4 460.50 0.27 325 129 132 3 475.88 3.64 326 129 133 4 460.52 0.27 327 130 133 3 475.04 2.50 328 130 134 4 463.28 1.19 329 131 134 3 471.91 2.37 330 131 135 4 464.16 1.51 331 132 135 3 480.23 2.21 332 132 136 4 463.39 1.12 333 133 136 3 477.09 3.78 334 133 137 4 464.62 0.51 335 134 137 3 473.63 0.45 336 134 138 4 460.62 0.13 337 135 138 3 479.28 2.38 338 136 140 4 494.56 1.17 339 137 140 3 491.80 2.55