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 5 455.57 4.54 2 2 73 71 31.20 0.12 3 2 76 74 25.96 0.35 4 2 127 125 23.59 0.04 5 2 128 126 23.59 0.05 6 2 131 129 23.00 0.34 7 3 6 3 479.23 2.16 8 3 7 4 469.29 2.27 9 4 7 3 471.17 1.33 10 4 8 4 469.50 2.17 11 5 8 3 481.84 0.85 12 5 9 4 474.45 0.31 13 6 9 3 477.72 1.21 14 6 10 4 474.47 0.33 15 6 124 118 48.09 0.55 16 6 127 121 48.16 0.50 17 7 10 3 476.95 1.59 18 7 11 4 474.45 0.34 19 7 73 66 48.67 0.64 20 7 74 67 48.75 0.68 21 8 11 3 475.56 0.65 22 8 12 4 469.23 2.94 23 9 12 3 477.06 0.10 24 9 13 4 469.23 2.95 25 9 120 111 67.39 0.90 26 9 121 112 67.19 0.82 27 9 124 115 67.09 0.80 28 10 13 3 492.06 0.40 29 10 14 4 464.36 0.52 30 10 70 60 67.17 0.82 31 10 124 114 67.28 0.85 32 10 125 115 67.18 0.81 33 10 128 118 67.14 0.83 34 11 14 3 478.88 1.02 35 11 15 4 464.37 0.53 36 11 70 59 67.45 0.95 37 11 71 60 67.47 0.94 38 11 73 62 67.45 0.95 39 12 15 3 468.24 2.46 40 12 16 4 468.24 2.46 41 13 16 3 477.81 1.42 42 13 17 4 465.69 0.12 43 13 113 100 77.70 0.01 44 13 121 108 67.74 0.91 45 13 125 112 67.70 0.91 46 14 17 3 465.69 0.12 47 14 18 4 465.69 0.12 48 14 21 7 376.97 1.79 49 14 63 49 67.69 0.92 50 14 66 52 67.66 0.93 51 14 67 53 67.66 0.93 52 14 70 56 67.64 0.94 53 15 18 3 471.73 1.58 54 16 113 97 89.32 4.68 55 16 116 100 87.81 3.98 56 17 20 3 482.35 0.62 57 17 21 4 433.38 4.70 58 17 24 7 393.78 6.98 59 17 109 92 87.82 3.98 60 17 113 96 96.66 1.17 61 18 21 3 495.86 2.06 62 20 23 3 470.12 0.65 63 20 24 4 468.97 0.07 64 21 24 3 468.06 0.54 65 21 25 4 464.19 2.46 66 21 63 42 98.09 1.41 67 22 25 3 468.06 0.54 68 22 26 4 468.06 0.53 69 22 60 38 105.80 0.14 70 22 63 41 103.73 1.19 71 23 26 3 469.37 2.51 72 23 27 4 468.68 2.85 73 23 56 33 118.64 0.14 74 24 27 3 482.82 4.22 75 24 28 4 468.68 2.85 76 24 108 84 119.20 0.12 77 24 109 85 120.31 0.42 78 24 112 88 130.49 0.02 79 25 28 3 473.26 0.56 80 25 29 4 469.00 2.69 81 25 59 34 118.59 0.17 82 25 63 38 118.07 0.08 83 26 29 3 474.60 0.11 84 26 30 4 469.00 2.69 85 26 55 29 129.54 0.09 86 26 56 30 129.62 0.12 87 26 59 33 123.92 2.46 88 27 30 3 467.73 2.06 89 27 31 4 465.37 1.19 90 27 108 81 131.75 0.01 91 27 112 85 132.58 0.16 92 28 31 3 473.74 0.95 93 28 32 4 467.37 2.23 94 28 101 73 131.49 0.10 95 28 104 76 131.53 0.07 96 28 105 77 131.49 0.10 97 28 108 80 131.80 0.02 98 29 32 3 477.21 1.91 99 29 33 4 465.72 3.06 100 29 55 26 132.00 0.07 101 29 58 29 131.80 0.03 102 29 59 30 131.71 0.07 103 29 101 72 131.53 0.08 104 30 33 3 485.41 0.53 105 30 34 4 465.64 3.10 106 30 50 20 133.09 0.30 107 31 34 3 478.82 2.76 108 31 35 4 460.93 0.99 109 31 104 73 131.90 0.07 110 31 107 76 132.84 0.34 111 31 108 77 132.89 0.33 112 32 35 3 478.82 2.76 113 32 36 4 456.35 1.30 114 32 39 7 318.81 2.81 115 32 101 69 131.89 0.06 116 32 104 72 132.50 0.22 117 33 37 4 440.96 1.51 118 33 39 6 341.44 19.57 119 33 40 7 285.44 1.34 120 33 43 10 284.06 0.65 121 33 48 15 133.25 0.36 122 33 55 22 133.22 0.35 123 34 37 3 482.88 0.90 124 36 39 3 486.66 3.42 125 36 100 64 132.37 0.18 126 36 103 67 133.07 0.34 127 36 104 68 133.08 0.34 128 37 40 3 482.18 1.00 129 38 41 3 487.61 1.55 130 39 42 3 487.61 1.55 131 39 43 4 490.39 0.14 132 39 97 58 131.88 0.04 133 39 100 61 133.06 0.34 134 40 43 3 494.28 1.80 135 40 44 4 480.03 2.10 136 40 48 8 253.43 4.55 137 41 44 3 498.08 0.10 138 42 93 51 132.66 0.33 139 42 94 52 133.02 0.34 140 42 97 55 133.09 0.34 141 43 46 3 480.52 2.23 142 43 48 5 452.62 0.68 143 43 58 15 240.02 0.99 144 45 54 9 250.27 2.88 145 46 54 8 250.26 2.88 146 46 55 9 250.27 2.88 147 46 58 12 250.21 2.91 148 47 52 5 268.03 5.96 149 47 54 7 250.28 2.88 150 47 55 8 250.31 2.89 151 48 52 4 422.25 5.28 152 48 55 7 250.28 2.87 153 49 52 3 474.35 0.07 154 52 55 3 477.06 2.81 155 52 56 4 460.51 7.44 156 53 56 3 463.56 5.92 157 53 57 4 461.52 6.94 158 54 57 3 480.91 2.75 159 54 58 4 472.47 1.46 160 55 58 3 473.70 2.00 161 55 59 4 464.11 2.80 162 56 59 3 474.35 1.68 163 56 60 4 471.19 0.74 164 57 60 3 484.92 3.71 165 57 61 4 471.19 0.74 166 58 61 3 473.42 0.38 167 58 62 4 471.16 0.74 168 59 62 3 479.26 2.79 169 59 63 4 471.13 0.75 170 60 63 3 471.52 1.00 171 60 64 4 468.75 1.90 172 61 64 3 469.20 2.16 173 61 65 4 463.50 4.56 174 62 65 3 483.15 0.40 175 62 66 4 470.34 1.15 176 62 101 39 162.87 2.33 177 63 66 3 478.30 2.83 178 63 67 4 469.63 0.78 179 64 67 3 475.68 1.52 180 64 68 4 464.58 1.76 181 65 68 3 469.66 0.78 182 65 69 4 464.61 1.76 183 65 80 15 159.35 0.39 184 65 83 18 159.35 0.39 185 66 69 3 475.26 3.56 186 66 70 4 464.61 1.76 187 66 105 39 180.75 4.25 188 66 128 62 180.69 4.21 189 66 129 63 180.58 4.24 190 66 132 66 178.75 5.04 191 67 70 3 469.92 4.04 192 67 71 4 464.61 1.76 193 68 71 3 475.06 1.20 194 68 72 4 464.56 1.73 195 68 79 11 230.94 9.64 196 69 72 3 475.39 1.37 197 69 73 4 463.06 4.80 198 69 76 7 303.71 11.57 199 69 80 11 215.22 10.13 200 69 128 59 183.12 3.05 201 69 132 63 180.65 4.20 202 70 73 3 470.31 1.19 203 70 128 58 190.83 0.79 204 72 75 3 471.41 0.30 205 72 76 4 420.67 6.59 206 72 79 7 278.07 1.17 207 73 76 3 481.90 0.34 208 75 78 3 475.12 1.03 209 75 79 4 433.94 16.25 210 76 79 3 468.80 1.18 211 76 80 4 421.91 12.54 212 76 128 52 198.00 3.87 213 76 131 55 197.93 3.85 214 76 132 56 196.99 3.37 215 76 135 59 196.87 3.42 216 77 81 4 392.90 15.32 217 77 135 58 196.86 3.43 218 78 81 3 476.30 2.15 219 80 83 3 480.17 0.21 220 80 84 4 467.53 2.67 221 80 132 52 198.44 3.91 222 80 135 55 198.26 3.84 223 80 136 56 198.31 3.85 224 81 84 3 478.21 1.19 225 81 85 4 472.18 4.88 226 81 139 58 198.22 3.86 227 82 85 3 483.69 0.60 228 82 86 4 478.88 1.53 229 83 86 3 478.90 1.54 230 83 87 4 478.89 1.54 231 83 136 53 198.46 3.89 232 84 87 3 483.48 0.76 233 84 88 4 472.19 4.88 234 84 135 51 198.46 3.89 235 84 136 52 198.46 3.89 236 84 138 54 198.40 3.90 237 84 139 55 198.22 3.85 238 85 88 3 483.47 0.76 239 85 89 4 453.69 4.38 240 85 139 54 198.22 3.86 241 86 89 3 485.32 0.17 242 86 90 4 453.59 4.33 243 86 91 5 414.51 15.20 244 87 91 4 398.18 14.45 245 87 92 5 371.44 1.07 246 87 93 6 338.90 11.36 247 87 98 11 290.76 2.21 248 87 136 49 198.49 3.91 249 88 92 4 365.70 1.78 250 88 139 51 198.29 3.85 251 88 140 52 198.09 3.83 252 89 92 3 492.90 3.16 253 93 97 4 480.31 0.93 254 93 98 5 474.87 3.58 255 94 97 3 495.75 2.32 256 95 98 3 481.23 0.68 257 96 99 3 491.43 5.77 258 96 100 4 480.06 1.06 259 97 100 3 479.62 1.22 260 97 101 4 479.62 1.22 261 98 101 3 485.39 1.42 262 98 102 4 469.06 0.77 263 98 133 35 199.38 3.79 264 98 136 38 199.41 3.79 265 98 137 39 199.37 3.79 266 99 102 3 475.69 2.35 267 99 103 4 473.29 1.35 268 100 103 3 476.57 2.99 269 100 104 4 468.14 0.35 270 101 104 3 470.46 3.68 271 101 105 4 459.57 0.75 272 102 105 3 471.89 2.16 273 102 106 4 461.25 1.59 274 102 129 27 199.99 3.58 275 102 133 31 199.98 3.58 276 103 106 3 466.33 3.06 277 103 107 4 463.36 0.54 278 104 107 3 464.69 1.19 279 104 108 4 461.70 0.29 280 105 108 3 472.23 2.46 281 105 109 4 461.69 0.29 282 105 129 24 201.65 3.69 283 106 109 3 469.90 3.80 284 106 110 4 464.24 1.56 285 106 117 11 225.91 14.13 286 106 122 16 203.45 3.16 287 106 125 19 201.77 3.70 288 106 126 20 201.77 3.74 289 106 129 23 201.66 3.69 290 107 110 3 474.02 1.43 291 107 111 4 464.24 1.56 292 108 111 3 473.29 2.96 293 108 112 4 461.98 2.69 294 109 112 3 479.81 1.83 295 109 113 4 456.26 0.16 296 109 125 16 203.66 3.09 297 110 113 3 480.94 2.40 298 110 117 7 262.68 4.25 299 113 116 3 477.86 0.55 300 113 117 4 446.13 1.43 301 114 117 3 483.51 1.45 302 115 118 3 526.28 0.91 303 116 121 5 456.94 0.23 304 117 121 4 457.50 0.52 305 117 122 5 456.91 0.21 306 117 125 8 411.66 6.26 307 118 121 3 468.25 1.48 308 118 122 4 461.91 1.69 309 119 122 3 467.41 1.05 310 119 123 4 461.91 1.69 311 120 123 3 475.18 1.99 312 120 124 4 460.12 0.80 313 121 124 3 468.38 4.88 314 121 125 4 468.14 5.00 315 122 125 3 474.85 1.78 316 122 126 4 474.82 1.78 317 123 126 3 474.85 1.78 318 123 127 4 474.83 1.78 319 124 127 3 474.82 1.66 320 124 128 4 468.84 1.22 321 125 128 3 475.35 2.04 322 125 129 4 468.84 1.22 323 126 129 3 487.70 4.13 324 126 130 4 465.66 2.85 325 127 130 3 475.13 4.01 326 127 131 4 466.57 2.39 327 128 131 3 475.13 4.01 328 128 132 4 461.42 0.20 329 129 132 3 475.88 3.64 330 129 133 4 461.46 0.18 331 130 133 3 470.67 4.69 332 130 134 4 461.51 0.15 333 131 134 3 471.91 2.37 334 131 135 4 461.51 0.15 335 132 135 3 480.23 2.21 336 132 136 4 461.50 0.14 337 133 136 3 476.43 4.11 338 133 137 4 462.59 0.51 339 134 137 3 473.63 0.45 340 134 138 4 461.54 0.15 341 135 138 3 479.28 2.38 342 137 140 3 475.28 4.13