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 5 462.78 4.15 2 2 73 71 25.11 0.65 3 2 127 125 26.25 0.60 4 2 128 126 25.63 0.91 5 2 131 129 25.11 0.65 6 3 6 3 472.53 0.72 7 3 7 4 467.30 1.89 8 4 7 3 470.17 0.46 9 4 8 4 470.29 3.39 10 5 8 3 470.99 3.04 11 5 9 4 470.30 3.39 12 6 9 3 484.65 3.78 13 6 10 4 470.33 3.37 14 6 124 118 47.22 0.53 15 6 127 121 46.97 0.53 16 7 10 3 485.38 4.15 17 7 11 4 470.33 3.37 18 7 73 66 50.87 0.25 19 7 74 67 50.87 0.25 20 8 11 3 483.38 3.15 21 8 12 4 470.31 3.36 22 9 12 3 478.31 1.36 23 9 13 4 467.35 1.97 24 9 120 111 61.90 1.22 25 9 121 112 61.88 1.21 26 9 124 115 61.83 1.22 27 10 13 3 483.54 0.55 28 10 14 4 467.35 1.97 29 10 70 60 61.84 1.22 30 10 124 114 61.86 1.22 31 10 125 115 61.84 1.22 32 10 128 118 61.79 1.19 33 11 14 3 483.89 1.54 34 11 15 4 472.19 4.42 35 11 70 59 61.84 1.22 36 11 73 62 61.84 1.22 37 12 15 3 487.55 0.29 38 12 16 4 483.89 1.54 39 13 16 3 483.89 1.54 40 13 17 4 483.89 1.54 41 13 121 108 63.84 0.56 42 13 125 112 62.23 1.36 43 14 17 3 481.56 2.58 44 14 18 4 467.27 1.98 45 14 21 7 450.84 1.54 46 14 63 49 63.95 0.52 47 14 66 52 62.23 1.37 48 14 67 53 62.19 1.38 49 14 70 56 62.19 1.38 50 15 18 3 473.14 2.04 51 16 116 100 73.42 1.97 52 17 20 3 494.84 4.07 53 17 21 4 456.31 0.81 54 17 24 7 446.58 0.88 55 17 109 92 74.18 1.56 56 17 113 96 79.52 0.89 57 18 21 3 489.41 4.36 58 20 23 3 468.32 0.12 59 20 24 4 463.79 2.45 60 21 24 3 479.30 3.33 61 21 25 4 468.43 0.17 62 21 63 42 79.35 0.97 63 22 25 3 476.42 3.87 64 22 26 4 467.43 0.68 65 22 60 38 79.56 0.93 66 22 63 41 79.53 0.93 67 23 26 3 488.89 1.11 68 23 27 4 472.06 3.00 69 24 27 3 475.88 0.37 70 24 28 4 470.38 2.19 71 24 108 84 129.23 0.09 72 24 109 85 129.22 0.09 73 24 112 88 133.09 0.97 74 25 28 3 482.90 1.47 75 25 29 4 471.24 1.76 76 25 59 34 126.33 1.39 77 26 29 3 481.98 1.49 78 26 30 4 471.25 1.77 79 26 55 29 128.71 0.49 80 26 56 30 129.47 0.12 81 26 59 33 126.47 1.46 82 27 30 3 477.36 1.28 83 27 31 4 471.25 1.77 84 27 108 81 133.69 0.91 85 27 112 85 134.02 0.96 86 28 31 3 476.94 1.37 87 28 32 4 471.24 1.78 88 28 101 73 133.50 0.84 89 28 104 76 133.52 0.84 90 28 105 77 133.51 0.85 91 28 108 80 133.78 0.96 92 29 32 3 471.23 1.79 93 29 33 4 467.53 0.07 94 29 55 26 133.83 1.01 95 29 58 29 133.75 1.01 96 29 59 30 133.72 1.00 97 29 62 33 133.75 0.97 98 29 101 72 133.62 0.91 99 30 33 3 481.44 3.62 100 30 34 4 466.94 3.63 101 31 34 3 478.72 1.14 102 31 35 4 466.78 3.71 103 31 104 73 133.69 0.91 104 31 107 76 133.97 0.94 105 31 108 77 133.99 0.94 106 32 35 3 482.60 0.98 107 32 36 4 459.98 2.25 108 32 39 7 320.20 1.06 109 32 101 69 133.69 0.92 110 32 104 72 133.90 0.91 111 33 37 4 395.43 2.88 112 33 39 6 315.11 1.48 113 33 40 7 285.75 0.43 114 33 43 10 284.36 1.12 115 33 48 15 134.06 0.92 116 33 55 22 134.04 0.92 117 34 37 3 489.78 3.33 118 36 39 3 493.05 2.56 119 36 100 64 133.74 0.92 120 36 104 68 134.04 0.96 121 37 40 3 485.38 1.28 122 38 41 3 499.72 4.49 123 39 42 3 494.00 4.29 124 39 43 4 482.28 0.46 125 39 97 58 133.71 0.94 126 39 100 61 133.99 0.94 127 40 43 3 488.99 3.67 128 40 48 8 194.31 27.72 129 41 44 3 484.78 1.56 130 42 93 51 133.65 0.92 131 42 94 52 133.84 0.88 132 42 97 55 133.93 0.89 133 43 46 3 470.54 2.86 134 43 48 5 400.81 8.15 135 43 58 15 192.33 28.14 136 45 54 9 195.16 27.57 137 46 54 8 195.13 27.59 138 46 55 9 195.13 27.58 139 46 58 12 195.07 27.62 140 47 52 5 273.23 2.22 141 47 54 7 195.16 27.57 142 47 55 8 195.16 27.57 143 48 55 7 195.12 27.57 144 49 52 3 485.04 1.04 145 52 55 3 487.19 0.72 146 52 56 4 466.41 2.58 147 53 56 3 480.10 4.27 148 53 57 4 467.93 1.80 149 54 57 3 484.91 1.28 150 54 58 4 469.07 1.19 151 55 58 3 488.34 3.00 152 55 59 4 469.08 1.19 153 56 59 3 488.60 2.87 154 56 60 4 482.89 5.72 155 57 60 3 485.47 1.30 156 57 61 4 476.50 2.52 157 58 61 3 473.18 0.85 158 58 62 4 473.20 0.87 159 59 62 3 487.95 3.20 160 59 63 4 478.84 1.27 161 60 63 3 484.05 1.34 162 60 64 4 478.84 1.27 163 61 64 3 484.14 1.29 164 61 65 4 478.85 1.26 165 62 65 3 484.06 1.34 166 62 66 4 478.30 4.21 167 63 66 3 474.56 0.89 168 63 67 4 473.06 1.63 169 64 67 3 476.16 3.19 170 64 68 4 476.15 3.19 171 65 68 3 476.15 3.19 172 65 69 4 475.60 3.46 173 65 83 18 140.53 3.72 174 66 69 3 475.61 3.46 175 66 70 4 467.38 0.65 176 66 105 39 192.07 3.75 177 66 129 63 176.52 3.35 178 66 132 66 157.73 4.98 179 67 70 3 479.19 1.68 180 67 71 4 472.45 1.89 181 68 71 3 476.50 3.00 182 68 72 4 472.70 1.77 183 69 72 3 475.22 3.01 184 69 73 4 457.97 3.16 185 69 76 7 307.49 0.52 186 69 80 11 222.16 3.31 187 69 128 59 192.08 3.75 188 69 132 63 172.06 1.10 189 70 73 3 472.72 1.76 190 70 128 58 192.31 3.64 191 72 75 3 471.81 2.22 192 72 76 4 446.50 4.54 193 72 79 7 288.06 2.41 194 73 76 3 485.22 1.53 195 73 128 55 208.75 2.72 196 75 78 3 485.37 1.46 197 75 79 4 453.56 4.31 198 76 79 3 471.04 4.44 199 76 80 4 426.38 4.14 200 76 128 52 210.67 2.36 201 76 131 55 209.45 2.67 202 76 132 56 209.48 2.69 203 76 135 59 209.44 2.68 204 77 81 4 426.26 3.50 205 77 135 58 209.30 2.60 206 77 140 63 185.95 0.80 207 78 81 3 475.68 2.08 208 80 83 3 476.79 1.67 209 80 84 4 473.31 3.42 210 80 132 52 211.19 2.20 211 80 135 55 211.11 2.16 212 80 136 56 211.03 2.12 213 81 84 3 473.33 3.41 214 81 85 4 473.31 3.42 215 81 140 59 203.66 0.84 216 82 85 3 481.81 3.37 217 82 86 4 473.31 3.41 218 83 86 3 479.24 4.65 219 83 87 4 473.26 3.40 220 83 136 53 211.19 2.18 221 84 88 4 447.51 2.02 222 84 89 5 447.51 2.02 223 84 135 51 211.21 2.21 224 84 136 52 211.16 2.18 225 84 138 54 211.12 2.18 226 84 140 56 210.74 2.27 227 85 89 4 391.98 25.73 228 85 90 5 391.97 25.73 229 86 90 4 368.64 3.21 230 86 91 5 311.35 5.75 231 87 91 4 311.32 5.76 232 87 92 5 310.07 6.38 233 87 93 6 306.73 8.05 234 87 98 11 286.18 1.01 235 87 136 49 211.30 2.20 236 88 92 4 306.74 8.04 237 88 136 48 211.34 2.22 238 88 137 49 211.28 2.20 239 88 138 50 211.28 2.20 240 88 139 51 211.18 2.16 241 89 92 3 488.47 1.14 242 89 139 50 211.19 2.17 243 93 97 4 470.26 0.01 244 93 98 5 472.26 1.75 245 94 97 3 490.59 2.14 246 95 98 3 481.01 0.41 247 95 99 4 483.67 0.92 248 95 137 42 211.78 2.19 249 96 99 3 490.55 2.52 250 96 100 4 476.08 2.88 251 97 100 3 476.07 2.88 252 97 101 4 473.03 1.36 253 98 101 3 472.94 5.78 254 98 102 4 464.76 2.52 255 98 133 35 211.97 2.12 256 98 136 38 212.05 2.18 257 98 137 39 211.96 2.14 258 99 102 3 474.68 4.92 259 99 103 4 465.60 2.10 260 100 103 3 480.56 1.97 261 100 104 4 473.20 1.71 262 101 104 3 476.49 0.45 263 101 105 4 472.01 2.30 264 102 105 3 477.60 0.49 265 102 106 4 460.34 0.23 266 102 129 27 212.45 2.27 267 103 106 3 478.16 0.21 268 103 107 4 470.92 2.26 269 104 107 3 476.19 0.37 270 104 108 4 460.43 0.28 271 105 108 3 473.80 0.83 272 105 109 4 472.68 0.28 273 105 129 24 214.50 2.60 274 106 109 3 476.25 2.04 275 106 110 4 476.26 2.04 276 106 117 11 230.36 3.87 277 106 122 16 215.82 2.79 278 106 125 19 215.19 2.48 279 106 126 20 215.16 2.50 280 106 129 23 215.04 2.48 281 107 110 3 476.26 2.04 282 107 111 4 476.26 2.04 283 108 111 3 476.27 2.04 284 108 112 4 476.27 2.04 285 109 112 3 477.34 1.95 286 109 113 4 453.46 6.78 287 109 117 8 267.93 4.59 288 109 125 16 217.24 2.98 289 110 114 4 440.42 0.27 290 110 117 7 258.43 0.10 291 111 114 3 490.30 4.72 292 113 116 3 477.15 0.29 293 113 117 4 451.12 7.46 294 114 117 3 486.16 2.46 295 115 118 3 516.61 0.96 296 116 121 5 443.12 5.39 297 117 122 5 432.09 0.13 298 117 125 8 423.53 4.15 299 118 121 3 477.27 1.92 300 118 122 4 458.21 7.61 301 119 122 3 477.58 1.76 302 119 123 4 472.42 0.81 303 120 123 3 475.45 0.09 304 120 124 4 474.64 0.30 305 121 124 3 477.16 0.94 306 121 125 4 474.64 0.30 307 122 125 3 481.69 1.32 308 122 126 4 474.63 0.29 309 123 126 3 480.39 0.67 310 123 127 4 477.13 0.95 311 124 127 3 477.87 1.93 312 124 128 4 471.76 0.54 313 125 128 3 477.71 2.10 314 125 129 4 463.07 3.92 315 126 129 3 482.66 4.09 316 126 130 4 463.07 3.93 317 127 130 3 476.91 0.90 318 127 131 4 472.70 0.90 319 128 131 3 473.01 1.05 320 128 132 4 472.69 0.90 321 129 132 3 468.80 2.93 322 129 133 4 468.55 2.79 323 130 133 3 477.74 3.40 324 130 134 4 468.72 2.87 325 131 134 3 477.87 1.55 326 131 135 4 468.85 2.89 327 132 135 3 478.48 1.84 328 132 136 4 468.93 2.93 329 133 136 3 478.48 1.84 330 133 137 4 472.04 1.28 331 134 137 3 486.29 1.43 332 134 138 4 472.04 1.28 333 135 138 3 479.09 2.17 334 135 140 5 471.39 1.57