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 5 464.09 0.36 2 2 73 71 32.38 1.51 3 2 127 125 23.38 0.49 4 2 128 126 22.15 0.12 5 3 6 3 478.06 0.88 6 3 7 4 469.44 3.01 7 4 7 3 474.59 0.45 8 4 8 4 471.23 3.88 9 5 8 3 477.52 0.73 10 5 9 4 464.16 0.35 11 6 9 3 486.99 1.38 12 6 10 4 466.49 0.85 13 6 124 118 53.67 0.43 14 7 10 3 481.56 1.04 15 7 11 4 475.59 1.46 16 7 73 66 55.73 0.28 17 7 74 67 57.15 0.93 18 8 11 3 485.39 3.45 19 8 12 4 475.49 1.39 20 9 12 3 483.87 1.53 21 9 13 4 475.49 1.39 22 9 124 115 64.08 3.15 23 10 13 3 475.76 1.52 24 10 14 4 468.81 1.96 25 10 70 60 64.13 3.13 26 10 73 63 64.36 3.02 27 10 124 114 64.09 3.16 28 10 125 115 64.08 3.16 29 10 128 118 64.03 3.18 30 11 14 3 486.43 0.85 31 11 15 4 478.50 2.50 32 11 70 59 64.19 3.10 33 11 73 62 64.41 3.01 34 12 15 3 482.68 0.43 35 12 16 4 486.36 3.27 36 13 16 3 491.90 1.79 37 13 17 4 486.36 3.27 38 13 121 108 65.01 3.23 39 13 125 112 65.00 3.22 40 14 17 3 478.50 2.50 41 14 18 4 478.50 2.50 42 14 21 7 395.78 1.57 43 14 66 52 67.39 2.04 44 14 67 53 65.06 3.21 45 14 70 56 65.06 3.21 46 14 109 95 87.66 1.18 47 15 18 3 473.29 0.33 48 16 113 97 101.34 1.59 49 16 116 100 98.14 0.04 50 17 20 3 489.53 2.50 51 17 21 4 457.54 5.20 52 17 24 7 410.67 7.74 53 17 109 92 101.31 1.60 54 17 113 96 101.89 1.34 55 18 21 3 493.95 2.56 56 20 23 3 480.34 0.78 57 20 24 4 470.39 0.90 58 21 24 3 483.12 0.61 59 21 25 4 472.69 0.26 60 21 63 42 104.43 0.42 61 21 67 46 104.42 0.42 62 22 25 3 480.30 0.79 63 22 26 4 477.03 2.43 64 22 59 37 115.66 2.41 65 22 60 38 114.74 1.95 66 23 26 3 486.13 0.83 67 23 27 4 470.68 0.12 68 24 27 3 477.26 3.09 69 24 28 4 470.67 0.13 70 24 108 84 126.84 0.86 71 24 109 85 129.08 1.40 72 24 112 88 137.33 0.81 73 25 28 3 483.23 2.29 74 25 29 4 473.34 2.66 75 25 59 34 123.49 0.34 76 25 62 37 122.45 0.58 77 26 29 3 473.40 2.64 78 26 30 4 473.39 2.62 79 26 55 29 139.25 0.14 80 26 56 30 137.34 0.82 81 26 59 33 131.47 0.01 82 27 30 3 475.05 1.80 83 27 31 4 473.42 2.62 84 27 108 81 140.18 0.03 85 27 112 85 141.35 0.51 86 28 31 3 484.09 4.14 87 28 32 4 470.27 1.04 88 28 101 73 139.72 0.07 89 28 104 76 139.72 0.07 90 28 105 77 139.74 0.09 91 28 108 80 140.22 0.03 92 29 32 3 476.53 1.09 93 29 33 4 474.31 0.97 94 29 55 26 141.22 0.50 95 29 58 29 141.04 0.41 96 29 59 30 140.50 0.15 97 30 33 3 487.68 2.21 98 30 34 4 467.75 0.21 99 30 50 20 142.31 0.79 100 30 55 25 141.30 0.52 101 31 34 3 482.55 3.14 102 31 35 4 467.93 0.01 103 31 104 73 141.32 0.62 104 31 107 76 141.89 0.80 105 31 108 77 141.53 0.60 106 31 111 80 142.26 0.80 107 32 35 3 484.19 3.96 108 32 36 4 457.90 5.01 109 32 39 7 302.97 5.87 110 32 101 69 141.30 0.62 111 32 104 72 141.47 0.63 112 33 37 4 419.68 4.00 113 33 39 6 309.08 3.16 114 33 40 7 283.74 4.19 115 33 43 10 283.74 4.19 116 33 48 15 142.46 0.77 117 33 55 22 142.31 0.79 118 34 37 3 487.54 2.27 119 34 50 16 142.59 0.70 120 36 39 3 503.97 2.93 121 36 100 64 141.37 0.64 122 36 103 67 142.09 0.86 123 36 104 68 142.09 0.86 124 37 40 3 491.10 0.55 125 38 41 3 495.95 0.82 126 39 42 3 496.70 0.00 127 39 43 4 494.69 1.01 128 39 97 58 141.34 0.64 129 39 100 61 142.06 0.87 130 40 43 3 496.70 0.00 131 40 48 8 233.84 3.74 132 41 44 3 506.16 0.92 133 42 91 49 141.41 0.68 134 42 92 50 141.44 0.69 135 42 93 51 141.44 0.69 136 42 94 52 141.56 0.73 137 42 97 55 142.12 0.85 138 43 46 3 492.83 0.56 139 43 48 5 395.98 24.75 140 43 58 15 230.69 4.62 141 45 54 9 243.20 0.98 142 46 54 8 243.20 0.98 143 46 58 12 233.92 3.62 144 47 52 5 247.00 2.74 145 47 54 7 243.21 0.98 146 47 55 8 243.21 0.98 147 48 55 7 243.21 0.98 148 49 52 3 477.00 4.00 149 52 55 3 487.76 1.97 150 52 56 4 468.30 2.06 151 53 56 3 469.24 1.59 152 53 57 4 465.16 2.48 153 54 57 3 471.39 0.51 154 54 58 4 461.56 4.29 155 55 58 3 468.14 1.01 156 55 59 4 465.11 2.53 157 56 59 3 465.91 2.93 158 56 60 4 465.22 2.56 159 57 60 3 478.44 0.79 160 57 61 4 475.87 2.09 161 58 61 3 478.68 0.91 162 58 62 4 476.11 2.20 163 59 62 3 482.41 0.58 164 59 63 4 476.12 2.21 165 60 63 3 483.64 0.04 166 60 64 4 476.12 2.21 167 61 64 3 477.71 3.00 168 61 65 4 477.39 1.56 169 62 65 3 478.26 2.00 170 62 66 4 477.36 1.53 171 63 66 3 480.78 0.18 172 63 67 4 477.35 1.53 173 64 67 3 481.75 0.31 174 64 68 4 470.75 1.79 175 65 68 3 478.89 0.83 176 65 69 4 477.35 1.52 177 65 83 18 174.05 1.60 178 66 69 3 487.70 3.66 179 66 70 4 477.34 1.52 180 66 105 39 184.34 2.04 181 66 128 62 186.38 1.89 182 66 129 63 183.96 1.88 183 66 132 66 182.59 2.50 184 67 70 3 481.71 0.66 185 67 71 4 475.99 2.19 186 68 71 3 480.75 0.18 187 68 72 4 475.98 2.20 188 68 79 11 225.77 1.83 189 68 80 12 219.84 2.79 190 69 72 3 472.73 0.57 191 69 73 4 465.57 2.88 192 69 76 7 275.89 0.88 193 69 80 11 217.34 1.55 194 69 128 59 189.79 0.24 195 69 132 63 182.72 2.54 196 70 73 3 477.48 1.81 197 70 128 58 191.09 0.41 198 72 75 3 478.75 2.46 199 72 76 4 461.21 3.29 200 72 79 7 279.21 6.99 201 73 76 3 478.75 2.46 202 73 128 55 197.47 1.24 203 75 78 3 485.86 1.12 204 75 79 4 473.10 0.84 205 76 79 3 481.42 2.90 206 76 80 4 465.53 2.94 207 76 131 55 200.31 0.23 208 76 132 56 200.33 0.24 209 76 135 59 199.90 0.03 210 77 81 4 465.52 2.94 211 77 135 58 200.32 0.24 212 78 81 3 485.86 0.10 213 80 83 3 473.55 0.10 214 80 84 4 469.80 1.18 215 80 132 52 210.69 2.43 216 80 135 55 209.96 2.23 217 80 136 56 209.98 2.23 218 81 84 3 473.39 0.18 219 81 85 4 470.29 1.42 220 82 85 3 489.06 2.50 221 82 86 4 473.86 0.42 222 83 86 3 479.38 2.33 223 83 87 4 473.87 0.42 224 83 136 53 210.81 2.43 225 84 87 3 483.87 0.09 226 84 88 4 468.52 1.84 227 84 135 51 210.87 2.44 228 84 136 52 210.81 2.43 229 84 138 54 210.81 2.43 230 85 88 3 491.89 3.06 231 85 89 4 456.97 7.52 232 85 90 5 455.31 8.35 233 85 139 54 210.79 2.44 234 86 90 4 406.06 0.83 235 86 91 5 390.69 3.21 236 87 91 4 356.31 1.20 237 87 92 5 352.29 3.12 238 87 93 6 340.96 8.76 239 87 98 11 280.12 4.86 240 87 136 49 210.93 2.45 241 88 92 4 352.27 3.12 242 88 136 48 211.08 2.47 243 88 139 51 210.84 2.43 244 88 140 52 210.80 2.44 245 89 92 3 478.88 2.56 246 89 139 50 210.94 2.47 247 92 140 48 211.11 2.41 248 93 97 4 483.91 0.94 249 93 98 5 478.81 1.36 250 93 140 47 211.18 2.44 251 94 97 3 490.94 0.93 252 94 98 4 487.82 2.48 253 95 98 3 485.50 1.10 254 95 137 42 211.29 2.40 255 95 140 45 211.22 2.43 256 96 99 3 484.55 0.62 257 96 100 4 484.07 0.95 258 97 100 3 484.07 0.95 259 97 101 4 480.93 2.43 260 98 101 3 484.07 0.95 261 98 102 4 472.94 4.62 262 98 133 35 211.99 2.17 263 98 136 38 211.99 2.17 264 98 137 39 211.96 2.16 265 99 102 3 485.16 1.50 266 99 103 4 472.94 4.62 267 100 103 3 485.54 1.31 268 100 104 4 463.31 3.00 269 101 104 3 483.49 3.27 270 101 105 4 460.98 1.84 271 102 105 3 471.65 2.66 272 102 106 4 469.23 3.10 273 102 129 27 212.66 2.34 274 103 106 3 482.73 3.64 275 103 107 4 467.02 4.21 276 104 107 3 469.23 3.10 277 104 108 4 467.03 4.19 278 105 108 3 478.66 1.60 279 105 109 4 467.05 4.20 280 105 129 24 213.38 2.43 281 106 109 3 472.69 1.19 282 106 110 4 466.86 4.10 283 106 117 11 232.94 3.30 284 106 122 16 214.91 2.48 285 106 125 19 213.69 2.44 286 106 126 20 213.63 2.42 287 106 129 23 213.50 2.39 288 107 110 3 481.28 3.10 289 107 111 4 472.69 1.20 290 108 111 3 477.89 1.41 291 108 112 4 468.28 3.40 292 109 112 3 481.10 2.36 293 109 113 4 459.98 1.54 294 109 117 8 250.78 5.62 295 109 125 16 215.34 2.04 296 110 114 4 440.25 0.79 297 110 117 7 250.78 5.62 298 111 114 3 493.45 0.38 299 113 116 3 475.92 0.90 300 113 117 4 453.53 1.10 301 114 117 3 478.73 1.46 302 115 118 3 515.60 2.75 303 116 121 5 449.06 3.28 304 117 121 4 449.77 3.64 305 117 122 5 449.06 3.28 306 117 125 8 436.55 1.27 307 118 121 3 456.43 0.32 308 118 122 4 452.69 2.18 309 119 122 3 468.32 5.63 310 119 123 4 456.36 0.35 311 120 123 3 480.18 6.79 312 120 124 4 463.71 0.73 313 121 124 3 471.73 0.67 314 121 125 4 463.71 0.73 315 122 125 3 476.43 0.64 316 122 126 4 463.72 0.72 317 123 126 3 473.15 0.66 318 123 127 4 471.54 0.94 319 124 127 3 471.85 1.09 320 124 128 4 463.73 0.71 321 125 128 3 472.07 1.21 322 125 129 4 463.77 0.69 323 126 129 3 477.29 0.77 324 126 130 4 461.94 0.23 325 127 130 3 483.61 1.17 326 127 131 4 466.66 0.59 327 128 131 3 477.38 1.95 328 128 132 4 466.84 0.66 329 129 132 3 466.99 0.59 330 129 133 4 473.42 3.95 331 130 133 3 473.57 3.88 332 130 134 4 473.42 3.95 333 131 134 3 479.03 1.14 334 131 135 4 473.43 3.94 335 132 135 3 479.03 1.14 336 132 136 4 473.43 3.94 337 133 136 3 465.03 0.27 338 133 137 4 458.38 3.58 339 134 137 3 483.18 3.42 340 134 138 4 457.62 3.23 341 135 138 3 463.24 3.73 342 137 140 3 480.63 0.24 343 137 141 4 461.93 2.81 344 138 141 3 472.64 2.45