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 5 443.66 1.33 2 2 73 71 30.66 0.68 3 2 76 74 25.84 0.41 4 2 127 125 22.42 0.05 5 2 128 126 22.19 0.04 6 2 131 129 22.12 0.07 7 3 6 3 475.94 0.52 8 3 7 4 474.42 0.34 9 4 7 3 474.45 0.34 10 4 8 4 474.44 0.34 11 5 8 3 481.84 0.84 12 5 9 4 474.44 0.34 13 6 9 3 477.73 1.21 14 6 10 4 474.32 0.40 15 6 124 118 47.93 0.47 16 6 127 121 47.98 0.45 17 7 10 3 476.82 1.66 18 7 11 4 469.24 2.94 19 7 73 66 50.26 0.16 20 7 74 67 50.27 0.15 21 8 11 3 474.67 0.20 22 8 12 4 469.19 2.92 23 9 12 3 475.56 0.64 24 9 13 4 469.14 2.91 25 9 121 112 59.77 0.04 26 9 124 115 59.77 0.04 27 10 13 3 486.09 2.59 28 10 14 4 469.10 2.92 29 10 70 60 59.76 0.07 30 10 124 114 59.79 0.05 31 10 125 115 59.74 0.06 32 10 128 118 59.74 0.06 33 11 15 4 449.31 2.06 34 11 70 59 59.77 0.07 35 11 71 60 59.91 0.14 36 11 73 62 59.77 0.07 37 12 15 3 469.57 1.80 38 12 16 4 469.56 1.80 39 13 16 3 482.35 0.85 40 13 17 4 466.59 1.27 41 13 113 100 81.77 0.24 42 13 121 108 60.95 0.27 43 13 125 112 60.85 0.32 44 14 17 3 479.50 5.17 45 14 18 4 462.23 3.45 46 14 21 7 414.41 3.41 47 14 63 49 74.94 0.66 48 14 66 52 60.85 0.32 49 14 67 53 66.92 3.35 50 14 70 56 60.84 0.32 51 15 18 3 475.89 1.80 52 16 113 97 91.62 1.92 53 16 116 100 91.53 1.91 54 17 20 3 478.25 1.44 55 17 21 4 436.12 3.52 56 17 24 7 406.29 11.39 57 17 109 92 88.58 0.42 58 17 113 96 96.65 1.17 59 18 21 3 495.86 2.06 60 20 23 3 475.54 2.06 61 20 24 4 464.25 2.50 62 21 24 3 468.12 0.57 63 21 25 4 464.25 2.50 64 21 63 42 98.45 1.21 65 22 25 3 470.61 0.90 66 22 26 4 468.12 0.57 67 22 60 38 99.39 0.92 68 22 63 41 99.23 0.98 69 23 26 3 482.82 4.22 70 23 27 4 463.46 2.12 71 24 27 3 482.82 4.22 72 24 28 4 464.29 1.71 73 24 108 84 117.53 0.42 74 24 109 85 120.49 0.34 75 24 112 88 128.38 1.06 76 25 28 3 473.26 0.56 77 25 29 4 470.66 1.85 78 25 59 34 116.61 0.85 79 25 63 38 116.56 0.84 80 26 29 3 474.60 0.11 81 26 30 4 467.35 0.21 82 26 55 29 126.69 0.99 83 26 56 30 125.36 1.48 84 26 59 33 116.61 0.83 85 27 30 3 476.44 2.30 86 27 31 4 467.35 0.20 87 27 108 81 130.85 0.26 88 27 112 85 132.45 0.24 89 28 31 3 469.38 1.23 90 28 32 4 465.69 1.03 91 28 101 73 128.72 1.17 92 28 104 76 128.73 1.18 93 28 105 77 128.73 1.17 94 28 108 80 131.04 0.35 95 29 32 3 474.67 1.42 96 29 33 4 459.36 0.07 97 29 55 26 130.52 0.41 98 29 58 29 130.52 0.41 99 29 59 30 128.88 1.23 100 29 101 72 128.81 1.21 101 30 33 3 480.93 1.71 102 30 34 4 466.11 3.27 103 30 50 20 132.78 0.20 104 31 34 3 482.74 1.86 105 31 35 4 465.38 1.21 106 31 104 73 132.03 0.31 107 31 107 76 132.41 0.21 108 31 108 77 132.65 0.22 109 31 111 80 132.93 0.25 110 32 35 3 472.98 0.17 111 32 36 4 456.66 1.46 112 32 39 7 241.86 23.31 113 32 100 68 132.02 0.32 114 32 101 69 132.02 0.32 115 32 104 72 132.06 0.30 116 33 37 4 407.95 6.59 117 33 39 6 306.88 1.73 118 33 40 7 231.36 28.37 119 33 43 10 157.38 2.63 120 33 48 15 132.94 0.26 121 33 55 22 132.93 0.26 122 36 39 3 485.84 3.00 123 36 100 64 132.12 0.33 124 36 103 67 132.86 0.23 125 36 104 68 132.85 0.21 126 37 40 3 480.01 0.08 127 38 41 3 487.44 1.63 128 39 42 3 488.01 1.50 129 39 43 4 494.28 1.80 130 39 97 58 132.00 0.33 131 39 100 61 132.78 0.21 132 40 43 3 494.28 1.80 133 40 48 8 149.19 1.13 134 41 44 3 498.08 0.10 135 42 93 51 131.87 0.26 136 42 94 52 132.47 0.07 137 42 97 55 132.79 0.21 138 43 46 3 477.99 0.97 139 43 48 5 458.27 1.89 140 43 58 15 142.93 0.37 141 45 54 9 149.76 1.03 142 46 54 8 149.72 1.02 143 46 55 9 149.72 1.01 144 46 58 12 149.71 1.02 145 47 52 5 234.16 39.24 146 47 54 7 149.77 1.03 147 47 55 8 149.78 1.02 148 48 52 4 396.62 18.09 149 48 55 7 160.71 6.46 150 49 52 3 475.97 0.88 151 51 56 5 465.92 4.81 152 52 55 3 466.97 4.37 153 52 56 4 465.94 4.82 154 53 56 3 465.94 4.82 155 53 57 4 471.85 1.85 156 54 57 3 471.92 1.83 157 54 58 4 472.56 1.49 158 55 58 3 472.60 1.46 159 55 59 4 472.60 1.46 160 56 59 3 474.35 1.68 161 56 60 4 472.56 1.45 162 57 60 3 483.80 4.28 163 57 61 4 471.21 0.77 164 58 61 3 473.59 0.29 165 58 62 4 471.19 0.77 166 59 62 3 479.19 2.83 167 59 63 4 471.03 0.76 168 60 63 3 473.59 2.03 169 60 64 4 470.39 1.07 170 61 64 3 472.00 1.26 171 61 65 4 465.10 3.76 172 62 65 3 483.15 0.40 173 62 66 4 470.36 1.14 174 62 101 39 146.95 5.49 175 63 66 3 478.30 2.83 176 63 67 4 466.61 0.74 177 64 67 3 478.30 2.83 178 64 68 4 466.61 0.74 179 65 68 3 468.79 0.34 180 65 69 4 466.61 0.74 181 65 80 15 147.05 5.33 182 65 83 18 136.78 0.42 183 66 69 3 477.03 2.68 184 66 70 4 463.72 0.70 185 66 105 39 183.03 2.64 186 66 129 63 157.72 0.34 187 66 132 66 157.58 0.30 188 67 70 3 471.40 3.29 189 67 71 4 459.63 1.34 190 68 71 3 475.06 1.20 191 68 72 4 459.18 1.56 192 68 79 11 167.28 1.59 193 69 72 3 475.39 1.37 194 69 73 4 459.08 1.53 195 69 76 7 293.33 3.24 196 69 80 11 157.65 0.33 197 69 128 59 245.22 5.54 198 69 132 63 161.25 1.42 199 70 73 3 470.31 1.19 200 70 128 58 251.59 2.31 201 72 75 3 471.42 0.29 202 72 76 4 442.43 14.20 203 72 79 7 310.02 14.17 204 73 76 3 479.49 1.53 205 75 78 3 479.88 1.34 206 75 79 4 466.38 0.02 207 76 79 3 475.65 3.46 208 76 80 4 447.86 5.96 209 76 128 52 271.02 0.81 210 76 131 55 268.12 0.56 211 76 132 56 266.58 1.10 212 76 135 59 265.20 0.46 213 77 80 3 477.05 2.76 214 77 81 4 440.91 2.48 215 77 135 58 266.68 0.12 216 78 81 3 469.18 1.42 217 80 83 3 479.44 0.58 218 80 84 4 449.94 3.78 219 80 132 52 271.50 0.99 220 80 135 55 271.33 1.04 221 80 136 56 271.33 1.04 222 81 84 3 469.48 0.73 223 81 85 4 474.98 3.52 224 81 139 58 271.35 1.04 225 82 85 3 480.49 1.10 226 82 86 4 478.92 1.55 227 83 86 3 483.52 0.74 228 83 87 4 483.51 0.75 229 83 136 53 272.12 1.30 230 84 87 3 485.94 1.63 231 84 88 4 483.51 0.74 232 84 135 51 272.19 1.28 233 84 136 52 272.11 1.29 234 84 138 54 272.07 1.31 235 84 139 55 272.02 1.30 236 85 88 3 486.94 0.96 237 85 89 4 474.82 5.08 238 85 139 54 272.04 1.30 239 86 89 3 485.32 0.17 240 86 90 4 453.82 0.47 241 86 91 5 435.25 4.09 242 87 91 4 425.85 0.60 243 87 92 5 402.49 12.28 244 87 93 6 340.33 14.52 245 87 98 11 289.52 2.83 246 87 136 49 272.26 1.25 247 87 140 53 272.05 1.30 248 88 92 4 395.41 14.62 249 88 139 51 272.07 1.31 250 88 140 52 271.86 1.23 251 89 92 3 492.91 3.16 252 92 140 48 272.17 1.29 253 93 97 4 477.34 0.56 254 93 98 5 471.75 2.24 255 93 140 47 272.38 1.29 256 94 97 3 487.45 0.42 257 95 98 3 484.59 1.01 258 95 140 45 272.43 1.30 259 96 99 3 492.31 5.33 260 96 100 4 484.06 2.08 261 97 100 3 480.88 0.48 262 97 101 4 476.39 1.76 263 98 101 3 485.39 1.42 264 98 102 4 475.10 1.12 265 98 133 35 273.01 1.28 266 98 136 38 273.02 1.28 267 98 137 39 273.00 1.28 268 98 140 42 272.84 1.21 269 99 102 3 474.56 0.71 270 99 103 4 470.26 1.28 271 100 103 3 473.29 1.35 272 100 104 4 469.14 0.72 273 101 104 3 469.13 0.72 274 101 105 4 466.04 0.81 275 102 105 3 471.69 2.03 276 102 106 4 466.05 0.80 277 102 129 27 273.61 1.31 278 102 133 31 273.20 1.26 279 103 106 3 478.63 5.50 280 103 107 4 466.04 0.80 281 104 107 3 475.19 4.06 282 104 108 4 464.13 1.73 283 105 108 3 472.44 2.35 284 105 109 4 464.20 1.77 285 105 129 24 274.16 1.28 286 106 109 3 472.62 2.44 287 106 110 4 461.62 0.48 288 106 117 11 275.18 1.29 289 106 122 16 274.35 1.34 290 106 125 19 274.32 1.33 291 106 126 20 274.33 1.34 292 106 129 23 274.29 1.32 293 107 110 3 472.31 2.28 294 107 111 4 461.92 2.92 295 108 111 3 473.10 2.67 296 108 112 4 461.21 3.27 297 109 112 3 465.18 1.05 298 109 113 4 452.73 0.21 299 109 125 16 274.80 1.39 300 110 117 7 275.27 1.33 301 113 116 3 477.86 0.55 302 113 117 4 446.12 1.42 303 114 117 3 481.58 2.41 304 115 118 3 526.28 0.91 305 116 121 5 451.14 2.67 306 117 121 4 457.50 0.52 307 117 122 5 451.14 2.67 308 117 125 8 412.05 6.45 309 118 121 3 467.40 1.06 310 118 122 4 459.35 0.41 311 119 122 3 465.68 0.20 312 119 123 4 463.11 1.48 313 120 123 3 475.18 1.99 314 120 124 4 464.00 1.93 315 121 124 3 474.72 1.71 316 121 125 4 463.04 1.45 317 122 125 3 476.53 2.62 318 122 126 4 474.72 1.72 319 123 126 3 474.84 1.78 320 123 127 4 474.72 1.72 321 124 127 3 474.72 1.72 322 124 128 4 466.18 0.12 323 125 128 3 473.62 2.91 324 125 129 4 467.88 0.73 325 126 129 3 487.70 4.13 326 126 130 4 468.89 1.24 327 127 130 3 481.29 0.93 328 127 131 4 468.89 1.24 329 128 131 3 478.31 2.42 330 128 132 4 466.34 2.52 331 129 132 3 475.88 3.64 332 129 133 4 466.33 2.51 333 130 133 3 475.72 2.17 334 130 134 4 463.50 1.12 335 131 134 3 465.49 2.15 336 131 135 4 464.38 1.59 337 132 135 3 474.12 5.26 338 132 136 4 465.38 0.90 339 133 136 3 467.12 0.55 340 133 137 4 464.63 0.52 341 134 137 3 481.11 1.46 342 134 138 4 464.63 0.52 343 135 138 3 481.11 1.46 344 136 140 4 489.82 1.20 345 137 140 3 485.50 0.97