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 5 439.63 0.57 2 2 73 71 31.77 0.18 3 2 76 74 26.63 0.05 4 2 127 125 22.40 0.08 5 2 128 126 22.39 0.08 6 3 6 3 474.33 0.29 7 3 7 4 474.47 0.33 8 4 7 3 474.48 0.33 9 4 8 4 474.47 0.33 10 5 8 3 477.06 1.54 11 5 9 4 474.45 0.34 12 6 9 3 477.72 1.21 13 6 10 4 474.45 0.34 14 6 124 118 46.81 0.10 15 6 127 121 46.95 0.10 16 7 10 3 476.95 1.59 17 7 11 4 474.44 0.34 18 7 73 66 50.66 0.35 19 7 74 67 50.94 0.42 20 8 11 3 474.31 0.40 21 8 12 4 469.18 2.94 22 9 12 3 477.05 0.10 23 9 13 4 472.13 1.43 24 9 121 112 63.45 0.12 25 9 124 115 63.16 0.27 26 10 13 3 486.09 2.59 27 10 14 4 469.12 2.93 28 10 70 60 63.51 0.12 29 10 124 114 63.45 0.12 30 10 125 115 63.16 0.27 31 10 128 118 63.15 0.28 32 11 14 3 477.94 1.49 33 11 15 4 459.19 7.88 34 11 70 59 63.53 0.12 35 11 71 60 63.88 0.03 36 11 73 62 63.88 0.03 37 12 15 3 466.76 3.22 38 12 16 4 460.33 6.43 39 13 16 3 477.82 1.42 40 13 17 4 469.56 1.81 41 13 113 100 79.20 1.52 42 13 121 108 64.02 0.05 43 13 125 112 64.02 0.05 44 14 17 3 469.56 1.81 45 14 18 4 470.14 2.10 46 14 21 7 405.35 3.18 47 14 63 49 68.00 0.58 48 14 66 52 64.02 0.06 49 14 67 53 64.02 0.07 50 14 70 56 64.01 0.07 51 15 18 3 471.73 1.58 52 16 113 97 95.46 1.50 53 16 116 100 93.95 0.76 54 17 20 3 484.95 0.68 55 17 21 4 427.09 7.69 56 17 24 7 388.74 4.73 57 17 109 92 93.84 0.74 58 17 113 96 95.72 1.60 59 18 21 3 493.20 3.39 60 20 23 3 473.48 1.03 61 20 24 4 468.06 0.53 62 21 24 3 468.98 0.07 63 21 25 4 464.19 2.46 64 21 63 42 98.06 1.49 65 22 25 3 468.99 0.08 66 22 26 4 464.19 2.46 67 22 60 38 105.42 0.04 68 22 63 41 98.93 1.11 69 23 26 3 474.77 0.20 70 23 27 4 461.88 1.31 71 24 27 3 482.82 4.22 72 24 28 4 465.32 1.19 73 24 108 84 117.81 0.07 74 24 109 85 117.84 0.06 75 24 112 88 122.23 1.64 76 25 28 3 473.26 0.56 77 25 29 4 468.67 2.85 78 25 59 34 118.07 0.08 79 25 63 38 117.36 0.28 80 26 29 3 474.60 0.11 81 26 30 4 465.40 1.20 82 26 55 29 122.02 1.72 83 26 56 30 121.80 1.66 84 26 59 33 118.25 0.01 85 27 30 3 465.72 1.05 86 27 31 4 467.40 2.21 87 27 108 81 122.75 1.55 88 27 112 85 123.67 1.76 89 28 31 3 474.67 1.42 90 28 32 4 466.05 1.57 91 28 101 73 122.54 1.49 92 28 104 76 122.55 1.49 93 28 105 77 122.54 1.49 94 28 108 80 122.92 1.48 95 29 32 3 474.67 1.42 96 29 33 4 459.04 0.04 97 29 55 26 123.56 1.77 98 29 58 29 123.55 1.77 99 29 59 30 123.17 1.77 100 29 101 72 122.60 1.52 101 30 33 3 480.93 1.71 102 30 34 4 459.05 0.04 103 30 50 20 124.01 1.76 104 31 34 3 469.28 2.05 105 31 35 4 452.90 3.02 106 31 104 73 122.88 1.48 107 31 107 76 123.59 1.74 108 31 108 77 123.71 1.74 109 32 35 3 474.70 0.30 110 32 36 4 451.72 3.62 111 32 39 7 314.66 2.77 112 32 101 69 122.75 1.45 113 32 104 72 123.03 1.50 114 33 37 4 426.89 8.64 115 33 39 6 336.04 11.60 116 33 40 7 311.23 1.54 117 33 43 10 287.76 10.20 118 33 48 15 124.08 1.75 119 33 55 22 124.02 1.76 120 34 37 3 491.92 5.42 121 36 39 3 486.66 3.42 122 36 100 64 122.87 1.49 123 36 103 67 123.81 1.72 124 36 104 68 123.81 1.72 125 37 40 3 480.01 0.08 126 38 41 3 482.70 1.18 127 39 42 3 487.59 1.54 128 39 43 4 494.28 1.80 129 39 97 58 122.75 1.44 130 39 100 61 123.75 1.69 131 40 43 3 494.28 1.80 132 40 44 4 478.06 1.91 133 40 48 8 253.62 4.46 134 41 44 3 498.08 0.10 135 42 45 3 647.43 0.54 136 42 93 51 122.59 1.46 137 42 94 52 123.49 1.71 138 42 97 55 123.68 1.67 139 43 46 3 476.79 1.56 140 43 48 5 422.19 8.93 141 43 58 15 244.81 4.43 142 45 54 9 251.78 3.52 143 46 54 8 251.69 3.48 144 46 55 9 251.68 3.47 145 46 58 12 251.55 3.53 146 47 52 5 251.89 3.50 147 47 54 7 251.85 3.48 148 47 55 8 251.84 3.48 149 48 52 4 412.08 1.19 150 48 55 7 251.90 3.51 151 49 52 3 474.93 1.40 152 52 55 3 473.57 1.06 153 52 56 4 465.84 4.78 154 53 56 3 471.75 1.82 155 53 57 4 465.85 4.78 156 54 57 3 471.76 1.82 157 54 58 4 472.47 1.47 158 55 58 3 472.46 1.46 159 55 59 4 472.55 1.49 160 56 59 3 474.35 1.68 161 56 60 4 472.63 1.47 162 57 60 3 483.97 4.20 163 57 61 4 472.62 1.47 164 58 61 3 474.88 0.35 165 58 62 4 472.62 1.47 166 59 62 3 481.25 1.80 167 59 63 4 472.50 1.49 168 60 63 3 471.54 0.99 169 60 64 4 465.66 1.36 170 61 64 3 471.45 1.53 171 61 65 4 461.82 3.27 172 62 65 3 483.15 0.40 173 62 66 4 465.11 3.77 174 62 101 39 134.44 6.04 175 63 66 3 470.31 1.17 176 63 67 4 467.38 2.62 177 64 67 3 472.43 0.10 178 64 68 4 470.36 1.14 179 65 68 3 475.24 3.58 180 65 69 4 468.17 0.04 181 65 83 18 125.28 1.47 182 66 69 3 475.25 3.57 183 66 70 4 466.62 0.74 184 66 105 39 157.19 0.45 185 66 129 63 155.09 0.82 186 66 132 66 135.35 5.65 187 67 70 3 471.56 3.21 188 67 71 4 470.39 1.16 189 68 71 3 475.34 1.32 190 68 72 4 470.39 1.16 191 68 79 11 224.80 0.32 192 69 72 3 475.42 1.35 193 69 73 4 470.31 1.19 194 69 76 7 245.11 4.32 195 69 80 11 154.58 0.85 196 69 128 59 181.19 5.98 197 69 132 63 154.65 0.82 198 70 73 3 470.31 1.19 199 70 128 58 170.66 0.53 200 72 75 3 477.29 2.64 201 72 76 4 446.98 0.90 202 72 79 7 268.12 3.33 203 73 76 3 477.29 2.64 204 75 78 3 475.12 1.03 205 75 79 4 459.63 1.15 206 76 79 3 465.66 0.39 207 76 80 4 445.06 4.80 208 76 128 52 220.96 0.39 209 76 131 55 220.39 0.65 210 76 132 56 211.20 0.23 211 77 81 4 414.10 6.28 212 77 135 58 211.18 0.24 213 78 81 3 469.17 1.42 214 80 83 3 480.17 0.21 215 80 84 4 457.71 2.33 216 80 132 52 221.59 0.34 217 80 135 55 221.24 0.33 218 81 84 3 473.72 3.43 219 81 85 4 463.12 0.38 220 81 139 58 221.28 0.34 221 82 85 3 483.79 0.55 222 82 86 4 466.43 0.03 223 83 86 3 483.82 0.57 224 83 87 4 474.88 5.07 225 83 136 53 221.72 0.35 226 84 87 3 483.86 0.58 227 84 88 4 474.88 5.07 228 84 135 51 221.75 0.35 229 84 136 52 221.72 0.35 230 84 138 54 221.71 0.34 231 84 139 55 221.69 0.34 232 85 88 3 478.64 3.19 233 85 89 4 468.98 8.01 234 85 139 54 221.69 0.34 235 86 89 3 485.34 0.16 236 86 90 4 457.61 2.33 237 86 91 5 438.75 2.33 238 87 91 4 419.53 2.56 239 87 92 5 367.98 28.32 240 87 93 6 347.94 18.34 241 87 98 11 289.51 2.82 242 87 136 49 221.94 0.30 243 87 140 53 221.69 0.33 244 88 92 4 368.01 28.34 245 88 139 51 221.73 0.34 246 88 140 52 221.67 0.32 247 89 92 3 490.06 1.74 248 92 140 48 221.87 0.28 249 93 97 4 482.50 0.33 250 93 98 5 480.22 1.47 251 93 140 47 221.96 0.30 252 94 97 3 495.75 2.32 253 94 98 4 484.89 0.86 254 95 98 3 492.97 3.18 255 95 140 45 222.06 0.33 256 96 99 3 494.80 4.09 257 96 100 4 481.04 0.57 258 97 100 3 480.94 0.53 259 97 101 4 479.59 1.20 260 98 101 3 479.60 1.48 261 98 102 4 474.47 0.77 262 98 133 35 222.66 0.14 263 98 136 38 222.75 0.18 264 98 137 39 222.72 0.18 265 98 140 42 222.74 0.18 266 99 102 3 474.58 0.72 267 99 103 4 474.47 0.77 268 100 103 3 474.49 0.77 269 100 104 4 474.48 0.77 270 101 104 3 475.72 1.05 271 101 105 4 470.24 1.34 272 102 105 3 474.69 0.53 273 102 106 4 466.08 0.75 274 102 129 27 223.27 0.27 275 102 133 31 223.16 0.30 276 103 106 3 470.84 0.29 277 103 107 4 465.05 1.27 278 104 107 3 476.98 3.17 279 104 108 4 466.47 2.08 280 105 108 3 472.54 2.30 281 105 109 4 466.47 2.10 282 105 129 24 223.60 0.40 283 106 109 3 472.72 2.39 284 106 110 4 462.42 0.07 285 106 117 11 226.30 0.67 286 106 122 16 224.27 0.28 287 106 125 19 224.16 0.33 288 106 126 20 224.12 0.35 289 106 129 23 223.88 0.26 290 107 110 3 472.11 2.38 291 107 111 4 457.14 0.49 292 108 111 3 472.83 2.81 293 108 112 4 458.20 1.05 294 109 112 3 470.17 1.44 295 109 113 4 452.82 0.26 296 109 125 16 224.53 0.27 297 110 113 3 480.96 1.26 298 110 117 7 226.30 0.67 299 113 116 3 477.86 0.55 300 113 117 4 435.56 4.24 301 114 117 3 480.09 1.67 302 115 118 3 526.28 0.91 303 116 121 5 463.94 3.69 304 117 121 4 465.24 3.04 305 117 122 5 463.94 3.69 306 117 125 8 422.33 0.65 307 118 121 3 468.31 1.51 308 118 122 4 465.25 3.04 309 119 122 3 468.31 1.51 310 119 123 4 465.25 3.04 311 120 123 3 473.75 1.20 312 120 124 4 465.26 3.04 313 121 124 3 474.74 1.70 314 121 125 4 458.13 0.53 315 122 125 3 474.43 1.98 316 122 126 4 462.47 1.42 317 123 126 3 474.42 1.98 318 123 127 4 462.47 1.41 319 124 127 3 471.73 3.21 320 124 128 4 465.85 0.29 321 125 128 3 474.00 2.71 322 125 129 4 467.89 0.73 323 126 129 3 482.05 1.31 324 126 130 4 467.89 0.73 325 127 130 3 481.29 0.93 326 127 131 4 467.89 0.73 327 128 131 3 475.84 5.00 328 128 132 4 465.61 2.08 329 129 132 3 475.88 3.64 330 129 133 4 464.01 2.04 331 130 133 3 473.01 1.62 332 130 134 4 459.77 0.71 333 131 134 3 465.45 2.16 334 131 135 4 460.11 0.39 335 132 135 3 474.12 5.26 336 132 136 4 461.32 0.21 337 133 136 3 477.09 3.78 338 133 137 4 460.47 0.56 339 134 137 3 475.47 1.36 340 134 138 4 459.90 2.15 341 135 138 3 475.81 1.20 342 136 140 4 491.44 0.39 343 137 140 3 485.50 0.97