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 5 458.46 0.04 2 2 73 71 28.82 0.30 3 2 127 125 21.45 0.04 4 2 128 126 21.44 0.04 5 2 131 129 21.43 0.04 6 3 6 3 473.44 1.31 7 3 7 4 461.29 0.99 8 4 7 3 476.75 0.35 9 4 8 4 470.17 5.41 10 5 8 3 480.11 0.44 11 5 9 4 471.42 2.31 12 6 9 3 480.93 1.65 13 6 10 4 464.40 1.20 14 6 124 118 48.28 1.02 15 6 127 121 48.28 1.02 16 7 10 3 479.69 0.23 17 7 11 4 467.62 3.04 18 7 73 66 48.90 0.75 19 7 74 67 48.91 0.75 20 8 11 3 482.13 5.07 21 8 12 4 467.63 3.04 22 9 12 3 480.13 0.33 23 9 13 4 468.42 2.64 24 9 120 111 63.04 0.18 25 9 121 112 62.55 0.36 26 9 124 115 62.54 0.38 27 10 13 3 480.07 0.36 28 10 14 4 468.35 2.66 29 10 70 60 62.53 0.37 30 10 124 114 62.57 0.38 31 10 125 115 62.54 0.36 32 10 128 118 62.51 0.38 33 11 14 3 480.06 0.36 34 11 15 4 472.34 2.04 35 11 70 59 62.50 0.39 36 11 73 62 62.52 0.38 37 12 15 3 483.66 0.92 38 12 16 4 482.63 1.44 39 13 16 3 488.36 3.27 40 13 17 4 484.25 0.62 41 13 113 100 75.12 1.89 42 13 121 108 70.30 3.31 43 13 125 112 63.31 0.18 44 14 17 3 486.75 1.87 45 14 18 4 484.25 0.62 46 14 63 49 70.27 3.29 47 14 66 52 63.33 0.17 48 14 67 53 63.51 0.07 49 14 70 56 63.27 0.20 50 14 109 95 74.98 1.85 51 15 18 3 485.15 2.67 52 16 113 97 75.30 1.90 53 16 116 100 75.24 1.94 54 17 20 3 480.00 3.27 55 17 21 4 474.19 3.12 56 17 24 7 392.86 2.16 57 17 109 92 75.33 1.89 58 18 21 3 491.25 0.20 59 20 23 3 483.18 0.65 60 20 24 4 469.12 0.20 61 21 24 3 488.14 3.12 62 21 25 4 462.63 0.78 63 21 63 42 94.23 1.38 64 21 64 43 94.25 1.39 65 22 25 3 479.68 1.10 66 22 26 4 461.75 0.32 67 22 60 38 104.34 0.41 68 23 26 3 485.83 1.98 69 23 27 4 464.41 1.01 70 23 112 89 136.55 0.09 71 24 27 3 470.18 0.45 72 24 28 4 464.78 2.26 73 24 108 84 128.16 1.28 74 24 112 88 136.55 0.09 75 25 28 3 470.19 0.45 76 25 29 4 465.69 2.69 77 25 59 34 118.90 0.79 78 25 63 38 114.11 0.36 79 26 29 3 472.35 0.70 80 26 30 4 465.04 2.19 81 26 55 29 136.25 0.51 82 26 56 30 136.25 0.50 83 26 59 33 127.31 3.15 84 27 30 3 472.93 0.18 85 27 31 4 470.06 0.29 86 27 108 81 137.44 0.23 87 27 112 85 137.87 0.10 88 28 31 3 472.93 0.18 89 28 32 4 470.75 0.06 90 28 101 73 137.28 0.20 91 28 104 76 137.41 0.22 92 28 105 77 137.27 0.20 93 28 108 80 137.69 0.12 94 29 32 3 474.94 1.04 95 29 33 4 470.77 0.05 96 29 55 26 137.81 0.07 97 29 58 29 137.81 0.07 98 29 59 30 137.77 0.07 99 29 62 33 137.75 0.07 100 29 101 72 137.44 0.24 101 30 33 3 484.56 3.77 102 30 34 4 470.07 0.30 103 30 50 20 138.19 0.04 104 31 34 3 478.52 2.83 105 31 35 4 465.97 2.35 106 31 104 73 137.84 0.04 107 31 107 76 137.99 0.07 108 31 108 77 138.05 0.08 109 31 111 80 138.27 0.06 110 32 35 3 473.81 2.23 111 32 36 4 455.04 3.58 112 32 39 7 292.82 0.25 113 32 43 11 292.81 0.23 114 32 100 68 137.84 0.03 115 32 101 69 137.84 0.04 116 32 104 72 137.97 0.07 117 33 37 4 419.66 4.04 118 33 39 6 325.13 3.98 119 33 40 7 289.31 1.48 120 33 43 10 289.31 1.48 121 33 48 15 138.28 0.08 122 33 55 22 138.21 0.06 123 34 37 3 484.26 0.48 124 36 39 3 493.50 0.35 125 36 100 64 137.91 0.07 126 36 103 67 138.11 0.09 127 36 104 68 138.18 0.07 128 37 40 3 484.72 1.76 129 38 41 3 487.57 0.22 130 39 42 3 492.32 1.17 131 39 43 4 485.21 0.40 132 39 97 58 137.86 0.04 133 39 100 61 138.08 0.07 134 40 43 3 485.21 0.40 135 40 44 4 478.66 0.73 136 40 48 8 291.98 0.97 137 41 44 3 496.24 0.24 138 42 45 3 643.52 0.99 139 42 93 51 137.66 0.12 140 42 94 52 137.90 0.02 141 42 97 55 138.11 0.04 142 43 46 3 489.49 2.11 143 43 48 5 445.37 7.87 144 43 58 15 138.34 0.03 145 45 54 9 195.30 25.94 146 46 54 8 195.24 25.97 147 46 55 9 195.23 25.97 148 46 58 12 195.22 25.97 149 47 52 5 283.50 5.26 150 47 54 7 195.31 25.94 151 47 55 8 195.30 25.94 152 48 55 7 197.14 25.02 153 49 52 3 471.92 2.41 154 51 56 5 450.74 1.39 155 52 55 3 476.81 1.58 156 52 56 4 464.76 0.66 157 53 56 3 470.07 3.31 158 53 57 4 464.36 0.87 159 54 57 3 471.00 0.31 160 54 58 4 465.08 1.24 161 55 58 3 474.04 1.89 162 55 59 4 464.29 1.63 163 56 59 3 471.69 1.03 164 56 60 4 467.64 0.04 165 57 60 3 472.18 0.19 166 57 61 4 467.64 0.04 167 58 61 3 476.30 1.87 168 58 62 4 467.66 0.04 169 59 62 3 477.61 2.98 170 59 63 4 467.57 0.08 171 60 63 3 474.44 1.15 172 60 64 4 467.55 0.07 173 61 64 3 476.03 1.93 174 61 65 4 460.79 3.40 175 62 65 3 476.01 1.94 176 62 66 4 469.73 1.21 177 62 101 39 156.86 2.92 178 63 66 3 476.42 3.35 179 63 67 4 470.25 1.47 180 64 67 3 474.80 1.76 181 64 68 4 470.25 1.47 182 65 68 3 474.02 2.15 183 65 69 4 470.25 1.48 184 65 83 18 154.71 3.62 185 66 69 3 482.14 7.44 186 66 70 4 470.23 1.49 187 66 105 39 177.84 2.27 188 66 128 62 218.52 1.05 189 66 129 63 193.62 11.28 190 66 132 66 173.77 2.73 191 67 70 3 476.78 1.79 192 67 71 4 470.22 1.48 193 68 71 3 477.75 1.30 194 68 72 4 467.00 3.07 195 68 79 11 226.68 19.53 196 69 72 3 468.59 2.06 197 69 73 4 450.87 1.49 198 69 76 7 266.47 1.89 199 69 80 11 201.88 7.16 200 69 128 59 226.37 4.67 201 69 132 63 201.89 7.16 202 70 73 3 471.85 1.02 203 70 128 58 221.32 2.15 204 72 75 3 464.12 0.22 205 72 76 4 394.19 5.98 206 72 79 7 289.49 0.42 207 73 76 3 470.32 1.18 208 73 128 55 240.40 7.04 209 75 78 3 483.70 2.71 210 75 79 4 461.74 0.99 211 76 79 3 471.56 1.61 212 76 80 4 460.20 0.24 213 76 128 52 242.39 6.88 214 76 131 55 242.30 6.86 215 76 132 56 241.93 6.67 216 76 135 59 241.80 6.66 217 77 80 3 474.38 0.88 218 77 81 4 464.68 5.04 219 77 135 58 241.80 6.66 220 78 81 3 474.25 0.45 221 80 83 3 475.42 0.17 222 80 84 4 462.69 5.73 223 80 132 52 243.00 6.73 224 80 135 55 242.87 6.68 225 80 136 56 242.87 6.68 226 81 84 3 475.01 2.33 227 81 85 4 470.81 1.69 228 81 139 58 242.88 6.68 229 82 85 3 474.64 0.23 230 82 86 4 474.63 0.23 231 83 86 3 474.64 0.23 232 83 87 4 474.64 0.22 233 83 136 53 243.05 6.74 234 84 87 3 475.47 0.18 235 84 88 4 474.64 0.22 236 84 135 51 243.03 6.75 237 84 136 52 243.03 6.75 238 84 139 55 242.99 6.73 239 85 88 3 475.46 0.19 240 85 89 4 459.50 7.35 241 85 139 54 243.00 6.74 242 86 89 3 479.31 0.38 243 86 90 4 446.99 4.03 244 86 91 5 446.63 4.21 245 87 91 4 418.15 10.04 246 87 92 5 418.14 10.04 247 87 93 6 399.43 19.39 248 87 98 11 274.66 2.79 249 87 136 49 243.11 6.73 250 87 140 53 243.05 6.74 251 88 92 4 417.10 10.56 252 88 139 51 243.05 6.74 253 88 140 52 242.97 6.74 254 89 92 3 488.40 0.53 255 89 139 50 243.09 6.74 256 92 140 48 243.11 6.73 257 93 97 4 473.88 1.96 258 93 98 5 469.32 2.23 259 93 140 47 243.46 6.57 260 94 97 3 490.84 1.98 261 95 98 3 484.97 1.40 262 95 137 42 243.77 6.55 263 95 140 45 243.66 6.58 264 96 99 3 485.88 1.19 265 96 100 4 475.97 0.19 266 97 100 3 481.81 0.18 267 97 101 4 469.05 2.03 268 98 101 3 478.75 1.35 269 98 102 4 465.50 0.26 270 98 133 35 244.28 6.44 271 98 136 38 244.31 6.45 272 98 137 39 244.28 6.43 273 98 140 42 244.24 6.42 274 99 102 3 477.50 2.33 275 99 103 4 474.09 4.04 276 100 103 3 477.88 2.52 277 100 104 4 465.44 0.23 278 101 104 3 474.03 4.08 279 101 105 4 465.30 0.28 280 102 105 3 475.83 5.00 281 102 106 4 463.47 4.54 282 102 129 27 244.86 6.29 283 102 133 31 244.80 6.29 284 103 106 3 477.08 2.56 285 103 107 4 464.84 5.28 286 104 107 3 473.87 0.78 287 104 108 4 472.44 0.06 288 105 108 3 472.45 0.07 289 105 109 4 472.44 0.06 290 105 129 24 245.19 6.18 291 106 109 3 471.92 0.21 292 106 110 4 462.62 4.85 293 106 117 11 245.94 6.29 294 106 122 16 245.52 6.20 295 106 125 19 245.50 6.21 296 106 126 20 245.44 6.18 297 106 129 23 245.42 6.19 298 107 110 3 473.41 0.55 299 107 111 4 470.37 8.72 300 108 111 3 476.05 5.89 301 108 112 4 470.37 8.72 302 109 112 3 481.17 3.33 303 109 113 4 449.56 3.25 304 109 125 16 245.73 6.30 305 110 113 3 475.72 6.05 306 110 117 7 245.94 6.29 307 113 116 3 466.88 0.34 308 113 117 4 368.75 3.26 309 115 118 3 533.73 0.58 310 116 121 5 447.20 5.19 311 117 121 4 447.20 5.19 312 117 122 5 434.70 1.02 313 117 125 8 417.19 7.33 314 118 121 3 461.75 1.35 315 118 122 4 449.45 4.79 316 119 122 3 465.63 4.99 317 119 123 4 456.15 1.45 318 120 123 3 464.22 0.33 319 120 124 4 456.16 1.45 320 121 124 3 462.11 1.53 321 121 125 4 456.38 3.93 322 122 125 3 471.31 2.92 323 122 126 4 464.70 0.23 324 123 126 3 474.15 1.16 325 123 127 4 464.78 0.20 326 124 127 3 467.03 1.32 327 124 128 4 464.77 0.19 328 125 128 3 470.56 3.08 329 125 129 4 464.76 0.18 330 126 129 3 469.76 0.04 331 126 130 4 459.82 5.01 332 127 130 3 473.59 7.17 333 127 131 4 459.82 5.01 334 128 131 3 469.81 5.61 335 128 132 4 463.12 3.36 336 129 132 3 467.84 1.02 337 129 133 4 457.02 0.23 338 130 133 3 465.05 3.79 339 130 134 4 457.03 0.22 340 131 134 3 465.05 3.79 341 131 135 4 457.03 0.22 342 132 135 3 467.06 1.50 343 132 136 4 459.41 0.98 344 133 136 3 460.75 1.65 345 133 137 4 460.75 1.65 346 134 137 3 476.91 6.55 347 134 138 4 457.14 2.12 348 135 138 3 463.04 0.83 349 136 140 4 483.61 1.25 350 137 140 3 478.51 1.81