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 5 455.56 4.52 2 2 73 71 30.77 0.63 3 2 76 74 25.95 0.35 4 2 127 125 22.65 0.42 5 2 128 126 22.18 0.20 6 3 6 3 474.33 0.29 7 3 7 4 474.44 0.34 8 4 7 3 481.18 3.02 9 4 8 4 474.44 0.35 10 5 8 3 481.83 0.84 11 5 9 4 474.44 0.35 12 6 9 3 477.72 1.21 13 6 10 4 469.22 2.95 14 6 124 118 47.21 0.81 15 6 127 121 47.20 0.78 16 7 10 3 476.82 1.66 17 7 11 4 469.22 2.94 18 7 73 66 47.80 1.07 19 7 74 67 50.68 0.36 20 8 11 3 474.69 0.21 21 8 12 4 469.51 2.79 22 9 12 3 475.56 0.65 23 9 13 4 469.18 2.94 24 9 121 112 63.48 0.10 25 9 124 115 63.48 0.11 26 10 13 3 478.88 1.02 27 10 14 4 457.82 3.77 28 10 70 60 63.55 0.10 29 10 124 114 63.54 0.09 30 10 125 115 63.48 0.10 31 10 128 118 63.47 0.11 32 11 14 3 477.94 1.49 33 11 15 4 462.62 6.17 34 11 70 59 63.59 0.11 35 11 71 60 63.61 0.11 36 11 73 62 63.88 0.03 37 12 15 3 469.56 1.82 38 12 16 4 469.55 1.82 39 13 16 3 477.82 1.42 40 13 17 4 469.56 1.82 41 13 113 100 79.64 0.94 42 13 121 108 64.01 0.06 43 13 125 112 64.00 0.06 44 14 17 3 465.06 0.43 45 14 18 4 463.89 0.15 46 14 21 7 400.69 4.73 47 14 66 52 64.00 0.06 48 14 67 53 64.00 0.06 49 14 70 56 64.00 0.06 50 14 109 95 79.62 0.93 51 15 18 3 471.73 1.58 52 16 113 97 89.37 3.06 53 16 116 100 89.27 3.10 54 17 20 3 482.35 0.62 55 17 21 4 430.34 4.54 56 17 24 7 430.35 4.55 57 17 109 92 89.31 3.08 58 17 113 96 89.89 2.87 59 18 21 3 492.40 3.47 60 20 23 3 473.49 1.04 61 20 24 4 469.06 0.12 62 21 24 3 472.43 1.56 63 21 25 4 468.13 0.57 64 21 63 42 98.69 1.02 65 22 25 3 469.06 0.11 66 22 26 4 468.14 0.57 67 22 60 38 99.53 0.87 68 22 63 41 99.52 0.87 69 23 26 3 480.27 5.50 70 23 27 4 464.41 2.44 71 23 56 33 118.52 0.45 72 24 27 3 481.81 4.73 73 24 28 4 462.36 1.42 74 24 108 84 121.31 0.96 75 24 109 85 126.80 1.78 76 24 112 88 133.23 1.39 77 24 113 89 133.24 1.39 78 25 28 3 469.92 1.11 79 25 29 4 465.53 0.70 80 25 59 34 118.52 0.45 81 25 63 38 116.93 0.38 82 26 29 3 469.39 1.23 83 26 30 4 465.53 0.70 84 26 55 29 128.62 3.10 85 26 56 30 128.61 3.10 86 26 59 33 118.39 0.53 87 27 30 3 474.38 3.33 88 27 31 4 461.82 1.16 89 27 108 81 133.46 1.47 90 27 112 85 134.59 1.31 91 28 31 3 470.83 0.82 92 28 32 4 466.05 1.57 93 28 101 73 133.28 1.41 94 28 104 76 133.28 1.40 95 28 105 77 133.29 1.40 96 28 108 80 133.56 1.44 97 29 32 3 469.06 1.79 98 29 33 4 463.67 2.04 99 29 55 26 134.28 1.45 100 29 58 29 134.20 1.47 101 29 59 30 134.13 1.50 102 29 101 72 133.37 1.43 103 30 33 3 485.40 0.53 104 30 34 4 463.67 2.04 105 30 50 20 134.77 1.43 106 31 34 3 476.56 1.23 107 31 35 4 461.31 0.88 108 31 104 73 134.29 1.46 109 31 107 76 134.71 1.32 110 31 108 77 134.75 1.34 111 31 111 80 134.94 1.34 112 32 35 3 477.00 1.85 113 32 36 4 461.23 0.83 114 32 39 7 278.17 2.85 115 32 101 69 134.30 1.46 116 32 104 72 134.53 1.33 117 33 37 4 423.45 3.06 118 33 39 6 338.39 20.89 119 33 40 7 266.02 0.37 120 33 43 10 257.38 3.94 121 33 48 15 134.97 1.33 122 36 39 3 489.42 1.21 123 36 100 64 134.31 1.47 124 36 103 67 134.84 1.36 125 36 104 68 134.91 1.34 126 37 40 3 480.01 0.08 127 38 41 3 481.81 0.98 128 39 42 3 488.14 1.43 129 39 43 4 487.55 1.56 130 39 97 58 134.30 1.48 131 39 100 61 134.77 1.34 132 40 43 3 494.28 1.80 133 40 48 8 187.95 27.41 134 41 44 3 494.29 1.80 135 42 92 50 134.59 1.38 136 42 93 51 134.59 1.39 137 42 94 52 134.70 1.35 138 42 97 55 134.82 1.33 139 43 46 3 485.06 1.76 140 43 48 5 419.22 17.38 141 43 58 15 175.53 21.58 142 45 54 9 192.42 29.43 143 46 54 8 192.41 29.43 144 46 58 12 192.38 29.43 145 47 52 5 277.69 13.20 146 47 54 7 192.44 29.43 147 47 55 8 192.44 29.42 148 48 55 7 210.12 20.59 149 49 52 3 480.78 3.28 150 52 55 3 466.25 4.00 151 52 56 4 472.59 1.43 152 53 56 3 474.06 2.16 153 53 57 4 472.59 1.42 154 54 57 3 472.60 1.42 155 54 58 4 472.59 1.42 156 55 58 3 473.86 1.92 157 55 59 4 472.58 1.44 158 56 59 3 474.35 1.68 159 56 60 4 472.63 1.45 160 57 60 3 483.97 4.20 161 57 61 4 472.60 1.46 162 58 61 3 474.88 0.35 163 58 62 4 472.59 1.46 164 59 62 3 474.86 0.34 165 59 63 4 472.52 1.50 166 60 63 3 472.53 1.50 167 60 64 4 471.88 1.81 168 61 64 3 472.50 1.50 169 61 65 4 474.06 0.72 170 62 65 3 483.15 0.40 171 62 66 4 470.34 1.15 172 63 66 3 478.30 2.83 173 63 67 4 461.48 0.12 174 64 67 3 464.99 1.54 175 64 68 4 459.74 1.08 176 65 68 3 469.55 0.74 177 65 69 4 464.98 1.54 178 65 80 15 154.53 1.71 179 65 83 18 154.25 1.84 180 66 69 3 475.24 3.58 181 66 70 4 462.05 0.07 182 66 105 39 162.84 1.97 183 66 128 62 167.81 0.67 184 66 129 63 161.30 1.42 185 66 132 66 157.60 0.29 186 67 70 3 474.18 1.90 187 67 71 4 469.67 3.89 188 68 71 3 475.32 1.33 189 68 72 4 473.91 1.77 190 68 79 11 189.72 16.46 191 69 72 3 475.39 1.37 192 69 73 4 467.41 2.63 193 69 76 7 282.62 4.11 194 69 80 11 182.07 11.95 195 69 128 59 180.38 4.32 196 69 132 63 158.33 0.06 197 70 73 3 467.74 2.47 198 70 128 58 180.05 4.12 199 72 75 3 471.41 0.29 200 72 76 4 408.65 5.00 201 72 79 7 272.18 1.43 202 73 76 3 479.46 1.52 203 75 78 3 483.22 0.32 204 75 79 4 461.26 1.81 205 76 79 3 470.36 1.17 206 76 80 4 424.92 15.31 207 76 128 52 214.14 11.96 208 76 131 55 214.05 12.01 209 76 132 56 214.03 12.00 210 77 81 4 409.45 23.05 211 77 135 58 214.00 12.00 212 78 81 3 469.17 1.43 213 80 83 3 480.80 0.53 214 80 84 4 469.83 3.00 215 80 132 52 214.94 12.16 216 80 135 55 214.93 12.16 217 80 136 56 214.93 12.16 218 81 84 3 478.20 1.19 219 81 85 4 478.86 1.52 220 81 139 58 214.84 12.17 221 82 85 3 480.10 0.91 222 82 86 4 478.87 1.51 223 83 86 3 483.45 0.78 224 83 87 4 477.41 3.79 225 83 136 53 214.98 12.18 226 84 87 3 483.47 0.78 227 84 88 4 477.40 3.80 228 84 135 51 214.99 12.18 229 84 136 52 214.97 12.18 230 84 138 54 214.96 12.18 231 84 139 55 214.89 12.20 232 85 88 3 478.64 3.19 233 85 89 4 474.88 5.04 234 85 139 54 214.88 12.19 235 86 89 3 483.52 0.73 236 86 90 4 449.60 3.65 237 86 91 5 440.05 1.69 238 87 91 4 425.38 8.55 239 87 98 11 236.21 4.41 240 87 136 49 215.01 12.17 241 87 140 53 214.87 12.19 242 88 139 51 214.94 12.17 243 88 140 52 214.83 12.18 244 93 97 4 471.75 2.24 245 93 98 5 471.96 2.14 246 93 140 47 215.45 12.02 247 94 97 3 484.87 0.86 248 95 98 3 480.14 0.84 249 95 140 45 215.95 12.12 250 96 99 3 483.34 2.44 251 96 100 4 470.26 1.28 252 97 100 3 475.21 1.04 253 97 101 4 465.06 1.31 254 98 101 3 477.85 2.35 255 98 102 4 473.28 1.35 256 98 133 35 217.15 11.87 257 98 136 38 217.19 11.85 258 98 137 39 217.16 11.87 259 98 140 42 217.25 11.81 260 99 102 3 476.77 1.81 261 99 103 4 474.47 0.77 262 100 103 3 474.57 0.71 263 100 104 4 474.47 0.77 264 101 104 3 476.92 0.46 265 101 105 4 474.47 0.77 266 102 105 3 471.66 2.04 267 102 106 4 470.25 1.33 268 102 129 27 218.02 11.78 269 102 133 31 217.97 11.76 270 103 106 3 470.01 1.22 271 103 107 4 469.16 0.81 272 104 107 3 470.38 0.20 273 104 108 4 468.50 1.09 274 105 108 3 472.37 2.39 275 105 109 4 469.68 1.69 276 105 129 24 219.94 11.02 277 106 109 3 472.54 2.48 278 106 110 4 470.23 1.44 279 106 117 11 230.64 11.79 280 106 122 16 221.31 10.91 281 106 125 19 220.46 11.11 282 106 126 20 220.46 11.11 283 106 129 23 220.37 11.14 284 107 110 3 474.68 3.67 285 107 111 4 470.23 1.44 286 108 111 3 471.55 5.23 287 108 112 4 469.38 6.32 288 109 112 3 482.75 0.36 289 109 113 4 454.78 0.74 290 109 125 16 221.17 11.09 291 110 113 3 479.50 1.68 292 110 117 7 256.81 1.28 293 113 116 3 479.80 0.42 294 113 117 4 462.86 6.95 295 114 117 3 482.03 0.70 296 115 118 3 524.59 0.06 297 116 121 5 455.11 2.75 298 117 121 4 465.19 3.02 299 117 122 5 455.10 2.75 300 117 125 8 423.25 0.35 301 118 121 3 468.25 1.48 302 118 122 4 462.95 1.17 303 119 122 3 465.68 0.19 304 119 123 4 465.67 0.19 305 120 123 3 468.67 1.30 306 120 124 4 465.67 0.19 307 121 124 3 474.43 1.99 308 121 125 4 469.39 4.37 309 122 125 3 474.87 1.78 310 122 126 4 474.73 1.70 311 123 126 3 477.88 0.28 312 123 127 4 474.89 1.77 313 124 127 3 477.88 0.28 314 124 128 4 474.76 1.70 315 125 128 3 478.38 0.53 316 125 129 4 468.91 1.24 317 126 129 3 482.05 1.31 318 126 130 4 468.91 1.24 319 127 130 3 477.24 1.10 320 127 131 4 466.14 0.14 321 128 131 3 475.13 4.01 322 128 132 4 463.65 1.10 323 129 132 3 475.88 3.64 324 129 133 4 461.29 0.03 325 130 133 3 470.68 4.69 326 130 134 4 464.05 1.38 327 131 134 3 471.91 2.37 328 131 135 4 471.49 2.16 329 132 135 3 480.23 2.21 330 132 136 4 466.99 0.10 331 133 136 3 476.44 4.11 332 133 137 4 461.44 0.07 333 134 137 3 475.47 1.36 334 134 138 4 460.00 0.44 335 135 138 3 475.81 1.20 336 136 140 4 489.82 1.20 337 137 140 3 485.50 0.97