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 5 443.79 1.51 2 2 73 71 28.56 1.19 3 2 127 125 23.04 0.45 4 2 128 126 21.93 0.09 5 2 131 129 21.17 0.12 6 3 6 3 468.98 2.97 7 3 7 4 443.98 1.42 8 3 127 124 33.42 0.88 9 4 7 3 477.98 1.88 10 4 8 4 453.86 0.07 11 5 8 3 480.94 0.40 12 5 9 4 464.62 5.18 13 6 9 3 471.19 4.48 14 6 10 4 465.81 4.62 15 6 124 118 45.58 0.01 16 6 127 121 45.54 0.01 17 7 10 3 482.06 0.96 18 7 11 4 466.98 4.04 19 7 73 66 45.59 0.03 20 7 74 67 47.26 0.79 21 8 11 3 476.16 0.55 22 8 12 4 470.41 2.33 23 9 12 3 476.24 0.30 24 9 13 4 465.79 4.63 25 9 121 112 54.20 0.03 26 9 124 115 54.18 0.04 27 10 13 3 470.40 2.33 28 10 14 4 464.54 5.20 29 10 70 60 54.18 0.04 30 10 124 114 54.20 0.03 31 10 125 115 54.19 0.04 32 10 128 118 54.17 0.04 33 11 15 4 450.98 0.13 34 11 70 59 54.16 0.03 35 11 71 60 54.19 0.04 36 12 15 3 473.55 0.18 37 12 16 4 461.96 5.61 38 13 16 3 481.82 0.58 39 13 17 4 461.55 5.16 40 13 113 100 81.85 0.24 41 13 121 108 60.43 2.83 42 13 125 112 54.53 0.06 43 14 17 3 462.57 5.67 44 14 18 4 461.55 5.16 45 14 66 52 54.50 0.03 46 14 67 53 54.50 0.03 47 14 70 56 54.50 0.03 48 14 109 95 81.19 0.51 49 15 18 3 466.04 3.95 50 16 113 97 87.45 2.50 51 16 116 100 82.72 0.17 52 17 20 3 483.42 1.45 53 17 21 4 436.12 6.58 54 17 24 7 389.55 1.21 55 17 109 92 81.95 0.24 56 17 113 96 87.50 2.49 57 18 21 3 481.99 0.30 58 20 23 3 470.38 0.78 59 20 24 4 454.27 0.13 60 21 24 3 461.41 3.71 61 21 25 4 452.73 0.24 62 21 63 42 94.08 0.64 63 22 25 3 469.56 0.37 64 22 26 4 452.79 0.26 65 22 60 38 99.44 2.08 66 22 63 41 95.34 0.01 67 23 26 3 475.31 0.47 68 23 27 4 452.31 0.51 69 23 56 33 118.54 0.79 70 24 27 3 469.65 3.02 71 24 28 4 461.69 5.21 72 24 108 84 123.73 1.31 73 24 109 85 127.06 2.39 74 24 112 88 132.05 2.54 75 24 113 89 132.26 2.48 76 25 28 3 468.08 2.02 77 25 29 4 465.56 3.28 78 25 59 34 118.86 0.63 79 26 29 3 468.78 1.68 80 26 30 4 460.93 5.59 81 26 55 29 128.03 3.39 82 26 56 30 127.62 3.60 83 26 59 33 120.33 0.97 84 27 30 3 467.51 2.31 85 27 31 4 465.51 3.29 86 27 108 81 132.53 2.56 87 27 112 85 132.84 2.62 88 28 31 3 466.69 2.65 89 28 32 4 465.44 3.27 90 28 101 73 132.46 2.54 91 28 104 76 132.49 2.56 92 28 105 77 132.49 2.56 93 28 108 80 132.63 2.57 94 29 32 3 468.70 1.64 95 29 33 4 464.77 2.92 96 29 55 26 132.85 2.64 97 29 58 29 132.85 2.64 98 29 59 30 132.71 2.57 99 29 62 33 132.69 2.58 100 29 101 72 132.53 2.55 101 30 33 3 483.87 3.18 102 30 34 4 464.77 2.92 103 30 50 20 133.12 2.62 104 30 51 21 133.11 2.62 105 31 34 3 469.35 3.20 106 31 35 4 455.71 1.58 107 31 104 73 132.53 2.56 108 31 107 76 132.84 2.62 109 31 108 77 132.85 2.62 110 32 35 3 474.25 0.76 111 32 36 4 445.06 3.49 112 32 39 7 300.02 1.77 113 32 101 69 132.53 2.56 114 32 104 72 132.75 2.60 115 33 37 4 408.14 10.00 116 33 39 6 312.38 4.41 117 33 40 7 277.21 2.78 118 33 43 10 274.37 4.20 119 33 48 15 133.26 2.67 120 36 39 3 490.32 0.76 121 36 100 64 132.69 2.65 122 36 103 67 132.94 2.61 123 36 104 68 132.95 2.62 124 37 40 3 473.81 1.86 125 38 41 3 480.88 0.28 126 39 42 3 484.91 1.52 127 39 97 58 132.53 2.56 128 39 100 61 132.84 2.62 129 40 43 3 481.30 0.29 130 40 44 4 471.00 0.47 131 40 48 8 192.47 26.77 132 41 44 3 489.30 0.69 133 42 92 50 132.48 2.59 134 42 93 51 132.48 2.58 135 42 94 52 132.63 2.60 136 42 97 55 132.82 2.61 137 43 46 3 477.38 0.99 138 43 48 5 448.95 3.29 139 43 58 15 191.31 26.37 140 45 54 9 192.53 26.62 141 46 54 8 192.50 26.61 142 46 58 12 192.49 26.61 143 47 52 5 278.88 10.37 144 47 54 7 192.72 26.70 145 47 55 8 192.72 26.69 146 48 52 4 352.31 0.81 147 48 55 7 195.40 25.87 148 49 52 3 466.14 5.78 149 52 55 3 466.99 3.64 150 52 56 4 434.70 4.12 151 53 56 3 456.29 9.54 152 53 57 4 434.70 4.12 153 54 58 4 468.03 4.76 154 55 58 3 476.45 0.55 155 55 59 4 465.44 6.07 156 56 59 3 475.05 1.26 157 56 60 4 475.05 1.26 158 57 60 3 475.06 1.26 159 57 61 4 475.05 1.26 160 58 61 3 475.06 1.26 161 58 62 4 475.04 1.25 162 59 62 3 475.28 1.13 163 59 63 4 461.75 3.66 164 60 63 3 475.10 0.41 165 60 64 4 461.74 3.67 166 61 64 3 463.82 2.62 167 61 65 4 460.39 3.00 168 62 65 3 469.76 0.35 169 62 66 4 462.17 2.94 170 63 66 3 464.21 1.93 171 63 67 4 462.00 3.03 172 64 67 3 462.18 2.94 173 64 68 4 466.60 1.66 174 65 68 3 468.99 0.47 175 65 69 4 468.98 0.47 176 65 83 18 160.88 6.25 177 66 69 3 466.63 1.64 178 66 70 4 466.63 1.64 179 66 105 39 177.59 5.83 180 66 128 62 190.16 0.46 181 66 129 63 177.84 5.62 182 66 132 66 177.23 5.89 183 67 70 3 466.63 1.64 184 67 71 4 466.64 1.63 185 68 71 3 471.45 3.00 186 68 72 4 459.59 1.90 187 68 79 11 207.22 9.48 188 69 72 3 466.96 5.58 189 69 73 4 452.40 5.34 190 69 76 7 317.55 8.69 191 69 80 11 169.22 2.19 192 69 128 59 190.22 0.45 193 69 132 63 177.60 5.72 194 70 73 3 474.31 3.19 195 70 128 58 190.23 0.45 196 72 75 3 475.41 1.70 197 72 76 4 402.13 11.30 198 72 79 7 307.55 13.58 199 73 76 3 481.28 4.64 200 75 78 3 481.35 1.26 201 75 79 4 440.03 13.20 202 76 79 3 470.81 1.04 203 76 80 4 434.59 10.47 204 76 128 52 245.82 11.92 205 76 131 55 242.78 10.80 206 76 132 56 241.86 11.19 207 76 135 59 241.75 11.20 208 77 81 4 432.50 11.53 209 77 135 58 241.71 11.21 210 78 81 3 464.94 4.69 211 80 83 3 475.05 2.92 212 80 84 4 464.33 1.80 213 80 132 52 247.68 12.73 214 80 135 55 247.56 12.78 215 80 136 56 247.58 12.78 216 81 84 3 482.20 3.19 217 81 85 4 482.86 3.52 218 81 139 58 247.56 12.78 219 82 85 3 484.09 2.90 220 82 86 4 471.39 2.21 221 83 86 3 471.41 2.21 222 83 87 4 464.60 1.18 223 83 136 53 247.82 12.79 224 84 88 4 461.43 0.35 225 84 135 51 247.86 12.78 226 84 136 52 247.81 12.79 227 84 138 54 247.82 12.79 228 85 88 3 462.42 0.14 229 85 89 4 445.92 1.20 230 85 90 5 441.21 5.85 231 85 139 54 247.77 12.76 232 86 89 3 468.99 1.83 233 86 90 4 425.92 13.50 234 86 91 5 404.10 6.12 235 87 91 4 404.10 6.12 236 87 92 5 355.66 18.08 237 87 93 6 323.26 1.89 238 87 98 11 315.03 5.97 239 87 136 49 247.91 12.77 240 87 140 53 247.86 12.79 241 88 92 4 365.80 12.98 242 88 139 51 247.86 12.79 243 88 140 52 247.59 12.78 244 89 92 3 459.29 5.72 245 89 139 50 247.87 12.79 246 92 140 48 247.89 12.79 247 93 97 4 475.79 4.22 248 93 98 5 475.79 4.22 249 93 140 47 247.97 12.77 250 94 97 3 484.29 3.17 251 94 98 4 481.12 1.56 252 94 140 46 248.01 12.78 253 95 98 3 481.35 1.44 254 95 99 4 481.12 1.56 255 95 137 42 248.08 12.79 256 96 99 3 481.35 1.45 257 96 100 4 471.34 3.33 258 97 100 3 473.28 2.37 259 97 101 4 473.28 2.36 260 98 101 3 474.49 2.96 261 98 102 4 468.22 0.36 262 98 133 35 248.22 12.75 263 98 136 38 248.27 12.77 264 99 102 3 473.04 2.77 265 99 103 4 468.24 0.37 266 100 103 3 473.06 2.76 267 100 104 4 468.25 0.36 268 101 104 3 474.14 3.34 269 101 105 4 467.76 0.62 270 102 105 3 467.86 0.58 271 102 106 4 469.48 1.48 272 102 129 27 248.43 12.81 273 103 106 3 475.94 1.16 274 103 107 4 469.50 1.47 275 104 107 3 467.80 0.60 276 104 108 4 467.58 0.51 277 105 108 3 467.59 0.51 278 105 109 4 465.30 0.64 279 105 129 24 249.66 12.54 280 106 109 3 470.06 1.73 281 106 110 4 458.60 1.37 282 106 117 11 250.97 12.53 283 106 122 16 250.12 12.53 284 106 125 19 250.02 12.54 285 106 126 20 249.89 12.48 286 106 129 23 249.75 12.52 287 107 110 3 470.44 1.54 288 107 111 4 459.72 0.82 289 108 111 3 480.59 4.71 290 108 112 4 466.28 2.46 291 109 112 3 472.43 5.53 292 109 113 4 453.64 3.85 293 109 125 16 250.08 12.52 294 110 113 3 474.72 4.38 295 110 117 7 253.68 13.21 296 113 116 3 473.13 1.93 297 113 117 4 435.67 2.64 298 114 117 3 481.81 0.81 299 115 118 3 530.28 2.91 300 116 121 5 437.30 4.16 301 117 122 5 418.21 13.70 302 117 125 8 386.25 14.77 303 118 121 3 468.56 1.32 304 118 122 4 447.20 4.98 305 119 122 3 462.88 0.48 306 119 123 4 460.55 1.69 307 120 123 3 467.75 1.73 308 120 124 4 464.99 0.53 309 121 124 3 461.29 1.33 310 121 125 4 460.54 1.70 311 122 125 3 476.04 5.04 312 122 126 4 464.94 0.51 313 123 126 3 478.81 3.66 314 123 127 4 464.94 0.51 315 124 127 3 467.63 0.84 316 124 128 4 464.17 0.89 317 125 128 3 471.11 1.65 318 125 129 4 465.88 1.74 319 126 129 3 473.67 2.16 320 126 130 4 462.64 1.61 321 127 130 3 478.78 2.19 322 127 131 4 462.64 1.60 323 128 131 3 466.03 0.10 324 128 132 4 462.61 1.58 325 129 132 3 479.88 1.64 326 129 133 4 463.36 1.08 327 130 133 3 470.94 1.44 328 130 134 4 465.62 0.04 329 131 134 3 468.34 0.39 330 131 135 4 465.63 0.05 331 132 135 3 468.50 0.30 332 132 136 4 461.88 1.93 333 133 136 3 471.69 2.26 334 133 137 4 462.60 1.55 335 134 137 3 469.56 1.58 336 134 138 4 455.73 2.46 337 135 138 3 463.44 1.98 338 137 140 3 479.28 2.14