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 5 443.69 1.32 2 2 73 71 31.74 0.14 3 2 76 74 26.44 0.62 4 2 127 125 22.81 0.31 5 2 128 126 21.98 0.04 6 3 6 3 475.94 0.52 7 3 7 4 459.11 7.33 8 4 7 3 474.56 0.28 9 4 8 4 474.44 0.33 10 5 8 3 474.56 0.29 11 5 9 4 474.44 0.34 12 6 9 3 475.22 0.04 13 6 10 4 460.79 7.17 14 6 124 118 46.69 0.24 15 6 127 121 46.69 0.24 16 7 10 3 474.55 0.29 17 7 11 4 469.23 2.94 18 7 73 66 48.67 0.64 19 7 74 67 50.67 0.36 20 8 11 3 474.67 0.20 21 8 12 4 469.16 2.91 22 9 12 3 475.56 0.64 23 9 13 4 469.13 2.91 24 9 121 112 63.47 0.12 25 9 124 115 63.16 0.27 26 10 13 3 478.88 1.02 27 10 14 4 464.18 0.42 28 10 70 60 63.52 0.12 29 10 124 114 63.52 0.13 30 10 125 115 63.48 0.11 31 10 128 118 63.16 0.27 32 11 14 3 477.06 1.93 33 11 15 4 464.33 0.35 34 11 70 59 63.57 0.10 35 11 71 60 63.80 0.01 36 11 73 62 63.76 0.01 37 12 15 3 468.43 2.38 38 12 16 4 469.55 1.82 39 13 16 3 482.35 0.85 40 13 17 4 471.18 1.01 41 13 113 100 79.27 0.80 42 13 121 108 64.56 0.32 43 13 125 112 64.56 0.32 44 14 17 3 479.50 5.17 45 14 18 4 466.77 0.90 46 14 21 7 412.03 0.43 47 14 63 49 69.95 0.83 48 14 66 52 64.55 0.33 49 14 67 53 64.56 0.33 50 14 70 56 64.55 0.33 51 15 18 3 476.02 1.74 52 16 113 97 93.98 0.72 53 16 116 100 93.94 0.71 54 17 20 3 482.39 0.60 55 17 21 4 456.18 6.48 56 17 24 7 411.91 13.86 57 17 109 92 91.30 0.60 58 17 113 96 95.73 1.59 59 18 21 3 495.86 2.06 60 20 23 3 475.54 2.06 61 20 24 4 467.02 1.13 62 21 24 3 468.14 0.57 63 21 25 4 463.88 2.69 64 21 63 42 98.39 1.33 65 22 25 3 469.05 0.12 66 22 26 4 468.13 0.57 67 22 60 38 98.97 1.15 68 22 63 41 98.95 1.13 69 23 26 3 483.22 4.03 70 23 27 4 463.88 2.69 71 24 27 3 480.26 5.50 72 24 28 4 466.43 1.41 73 24 108 84 118.56 1.67 74 24 109 85 120.97 1.14 75 24 112 88 128.29 1.29 76 25 28 3 470.69 0.72 77 25 29 4 470.66 1.85 78 25 59 34 116.23 1.04 79 25 63 38 113.45 0.34 80 26 29 3 474.60 0.11 81 26 30 4 467.38 0.21 82 26 55 29 125.62 1.60 83 26 56 30 125.61 1.60 84 26 59 33 120.33 1.03 85 27 30 3 474.42 3.31 86 27 31 4 467.37 0.21 87 27 108 81 129.21 1.27 88 27 112 85 131.27 0.63 89 28 31 3 467.38 0.21 90 28 32 4 465.35 1.23 91 28 101 73 128.71 1.18 92 28 104 76 128.86 1.26 93 28 105 77 128.71 1.18 94 28 108 80 129.50 1.12 95 29 32 3 473.66 1.93 96 29 33 4 459.14 0.09 97 29 55 26 130.31 0.71 98 29 58 29 129.11 1.31 99 29 59 30 128.89 1.23 100 29 101 72 128.88 1.25 101 30 33 3 479.87 1.18 102 30 34 4 459.14 0.09 103 30 50 20 131.25 0.60 104 31 34 3 475.07 1.22 105 31 35 4 459.09 0.07 106 31 104 73 130.19 0.77 107 31 107 76 131.19 0.60 108 31 108 77 131.21 0.60 109 32 35 3 472.95 0.58 110 32 36 4 443.12 0.72 111 32 39 7 248.13 32.76 112 32 100 68 130.17 0.76 113 32 101 69 130.13 0.76 114 32 104 72 130.75 0.56 115 33 37 4 405.05 12.26 116 33 39 6 248.27 32.70 117 33 40 7 158.62 2.04 118 33 43 10 158.64 2.04 119 33 48 15 131.28 0.62 120 36 39 3 486.72 3.39 121 36 100 64 130.43 0.65 122 36 103 67 131.27 0.63 123 36 104 68 131.33 0.63 124 37 40 3 480.00 0.09 125 38 41 3 487.93 1.44 126 39 42 3 486.45 0.97 127 39 43 4 489.88 4.00 128 39 97 58 130.13 0.76 129 39 100 61 131.33 0.62 130 40 43 3 494.28 1.80 131 40 48 8 141.58 3.69 132 41 44 3 494.29 1.80 133 42 45 3 646.64 0.14 134 42 93 51 129.81 0.60 135 42 94 52 131.30 0.58 136 42 97 55 131.38 0.61 137 43 46 3 477.87 1.02 138 43 48 5 452.62 0.68 139 43 58 15 140.00 4.28 140 45 54 9 142.65 3.48 141 46 54 8 142.64 3.48 142 46 55 9 142.63 3.48 143 46 58 12 142.59 3.47 144 47 52 5 231.28 40.68 145 47 54 7 142.65 3.48 146 47 55 8 142.65 3.48 147 48 52 4 382.45 12.06 148 48 55 7 171.60 1.29 149 49 52 3 475.97 0.88 150 51 56 5 454.96 0.65 151 52 55 3 471.82 1.78 152 52 56 4 470.25 2.56 153 53 56 3 470.25 2.56 154 53 57 4 460.93 3.60 155 54 57 3 471.87 1.76 156 54 58 4 461.34 3.46 157 55 58 3 472.54 1.41 158 55 59 4 462.00 3.79 159 56 59 3 474.35 1.68 160 56 60 4 471.12 0.71 161 57 60 3 483.80 4.28 162 57 61 4 471.11 0.72 163 58 61 3 473.34 0.42 164 58 62 4 462.13 3.77 165 59 62 3 479.26 2.79 166 59 63 4 461.40 3.41 167 60 63 3 471.26 1.51 168 60 64 4 457.96 1.70 169 61 64 3 472.00 1.26 170 61 65 4 463.59 4.51 171 62 65 3 483.15 0.40 172 62 66 4 467.17 2.73 173 62 101 39 153.00 2.46 174 63 66 3 467.17 2.73 175 63 67 4 467.16 2.73 176 64 67 3 470.36 1.14 177 64 68 4 465.02 1.53 178 65 68 3 475.23 3.58 179 65 69 4 465.03 1.53 180 65 80 15 153.35 2.41 181 65 83 18 153.31 2.39 182 66 69 3 475.25 3.57 183 66 70 4 465.03 1.54 184 66 105 39 177.50 5.57 185 66 129 63 157.62 0.29 186 66 132 66 157.56 0.31 187 67 70 3 475.34 1.32 188 67 71 4 470.39 1.15 189 68 71 3 475.35 1.32 190 68 72 4 470.40 1.15 191 68 79 11 167.92 1.31 192 69 72 3 475.41 1.36 193 69 73 4 470.31 1.19 194 69 76 7 227.03 27.72 195 69 80 11 162.06 2.57 196 69 128 59 188.10 0.46 197 69 132 63 163.34 2.56 198 70 73 3 470.31 1.18 199 70 128 58 188.12 0.48 200 72 75 3 472.37 0.18 201 72 76 4 399.58 7.23 202 72 79 7 310.78 8.64 203 73 76 3 479.49 1.53 204 75 78 3 479.88 1.34 205 75 79 4 449.90 3.87 206 76 79 3 461.43 2.50 207 76 80 4 448.87 3.35 208 76 128 52 271.22 0.91 209 76 131 55 269.31 0.05 210 76 132 56 265.26 0.43 211 76 135 59 265.24 0.45 212 77 80 3 473.33 0.26 213 77 81 4 448.87 3.35 214 77 135 58 265.24 0.45 215 78 81 3 472.38 0.18 216 80 83 3 480.73 0.07 217 80 84 4 466.17 1.82 218 80 132 52 271.38 0.94 219 80 135 55 271.33 0.95 220 80 136 56 271.33 0.96 221 81 84 3 472.22 4.84 222 81 85 4 472.24 4.84 223 81 139 58 271.33 0.96 224 82 85 3 480.12 0.92 225 82 86 4 474.22 3.87 226 83 86 3 475.38 3.29 227 83 87 4 474.21 3.87 228 83 136 53 271.62 1.05 229 84 87 3 483.48 0.76 230 84 88 4 483.45 0.76 231 84 135 51 271.66 1.06 232 84 136 52 271.62 1.05 233 84 138 54 271.62 1.05 234 84 139 55 271.60 1.06 235 85 88 3 483.47 0.76 236 85 89 4 447.50 4.71 237 85 139 54 271.58 1.06 238 86 90 4 387.44 16.71 239 86 91 5 361.24 19.23 240 87 91 4 345.29 11.84 241 87 92 5 304.57 8.52 242 87 93 6 304.56 8.52 243 87 98 11 278.68 2.60 244 87 136 49 271.77 1.06 245 87 140 53 271.58 1.07 246 88 92 4 311.02 5.29 247 88 139 51 271.63 1.06 248 88 140 52 271.58 1.07 249 89 92 3 490.06 1.74 250 93 97 4 482.23 0.20 251 93 98 5 474.93 3.62 252 93 140 47 271.81 1.04 253 94 97 3 495.75 2.32 254 94 98 4 484.62 0.99 255 95 98 3 492.97 3.18 256 95 140 45 271.87 1.05 257 96 99 3 492.31 5.33 258 96 100 4 481.05 0.57 259 97 100 3 480.95 0.52 260 97 101 4 480.95 0.52 261 98 101 3 485.39 1.42 262 98 102 4 469.81 1.55 263 98 133 35 272.24 0.99 264 98 136 38 272.25 1.00 265 98 137 39 272.24 1.00 266 98 140 42 272.23 1.00 267 99 102 3 477.85 2.35 268 99 103 4 473.29 1.35 269 100 103 3 477.50 2.52 270 100 104 4 473.29 1.35 271 101 104 3 471.22 2.50 272 101 105 4 464.64 0.80 273 102 105 3 470.98 2.39 274 102 106 4 459.73 1.67 275 102 129 27 272.80 0.91 276 102 133 31 272.58 0.99 277 103 106 3 470.84 0.29 278 103 107 4 462.44 0.07 279 104 107 3 476.98 3.17 280 104 108 4 466.49 2.09 281 105 108 3 480.23 1.54 282 105 109 4 466.47 2.10 283 105 129 24 273.42 0.90 284 106 109 3 472.72 2.39 285 106 110 4 466.47 2.10 286 106 117 11 274.23 1.05 287 106 122 16 273.55 0.95 288 106 125 19 273.55 0.95 289 106 126 20 273.53 0.94 290 106 129 23 273.44 0.90 291 107 110 3 474.03 1.43 292 107 111 4 463.31 1.10 293 108 111 3 474.81 1.81 294 108 112 4 463.37 3.91 295 109 112 3 469.24 0.97 296 109 113 4 447.00 3.18 297 109 125 16 273.87 1.04 298 110 117 7 274.37 1.12 299 113 116 3 477.86 0.55 300 113 117 4 454.62 11.06 301 114 117 3 480.09 1.67 302 115 118 3 526.28 0.91 303 116 121 5 463.88 3.72 304 117 121 4 463.89 3.71 305 117 122 5 463.88 3.71 306 117 125 8 420.27 10.59 307 118 121 3 466.37 2.48 308 118 122 4 466.37 2.48 309 119 122 3 472.99 0.83 310 119 123 4 466.38 2.48 311 120 123 3 475.24 1.96 312 120 124 4 466.38 2.48 313 121 124 3 474.87 1.77 314 121 125 4 463.69 1.13 315 122 125 3 474.44 1.99 316 122 126 4 472.16 3.12 317 123 126 3 474.43 1.98 318 123 127 4 471.84 3.27 319 124 127 3 474.83 1.67 320 124 128 4 471.85 3.15 321 125 128 3 474.00 2.71 322 125 129 4 467.88 0.73 323 126 129 3 484.02 0.33 324 126 130 4 467.89 0.73 325 127 130 3 475.13 4.01 326 127 131 4 464.02 2.06 327 128 131 3 478.31 2.42 328 128 132 4 465.61 2.08 329 129 132 3 475.88 3.64 330 129 133 4 464.01 2.04 331 130 133 3 474.91 2.57 332 130 134 4 462.37 1.64 333 131 134 3 467.80 0.99 334 131 135 4 462.38 1.64 335 132 135 3 475.73 4.46 336 132 136 4 464.62 0.51 337 133 136 3 476.44 4.11 338 133 137 4 463.91 0.15 339 134 137 3 475.47 1.36 340 134 138 4 463.91 0.15 341 135 138 3 481.11 1.46 342 136 140 4 489.82 1.20 343 137 140 3 485.50 0.97