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 5 457.25 3.68 2 2 73 71 30.95 0.61 3 2 127 125 27.48 1.10 4 2 128 126 24.03 0.27 5 3 6 3 477.69 1.39 6 3 7 4 470.95 3.15 7 3 127 124 37.07 0.06 8 4 7 3 476.72 0.27 9 4 8 4 475.74 0.76 10 5 8 3 478.69 0.72 11 5 9 4 476.19 0.53 12 6 9 3 479.38 0.29 13 6 10 4 473.95 0.58 14 6 124 118 49.76 0.03 15 6 127 121 49.57 0.12 16 7 10 3 476.07 0.47 17 7 11 4 473.94 0.58 18 7 73 66 51.56 0.94 19 7 74 67 52.42 0.51 20 8 11 3 475.82 0.35 21 8 12 4 470.98 2.06 22 9 12 3 477.31 0.24 23 9 13 4 470.94 2.06 24 9 121 112 57.34 0.29 25 9 124 115 56.20 0.07 26 10 13 3 479.70 2.35 27 10 14 4 470.89 2.04 28 10 70 60 57.50 0.58 29 10 124 114 56.22 0.07 30 10 125 115 56.19 0.07 31 10 128 118 56.18 0.07 32 11 14 3 471.48 1.74 33 11 15 4 470.88 2.04 34 11 70 59 56.20 0.06 35 12 15 3 461.00 6.09 36 12 16 4 460.99 6.09 37 13 16 3 479.57 0.54 38 13 17 4 456.88 4.03 39 13 121 108 59.84 1.27 40 13 125 112 59.76 1.28 41 14 17 3 470.27 1.45 42 14 18 4 456.84 4.02 43 14 63 49 62.07 0.16 44 14 66 52 59.76 1.30 45 14 67 53 59.76 1.30 46 14 70 56 59.76 1.30 47 14 105 91 69.12 0.46 48 14 109 95 75.92 1.73 49 14 125 111 59.86 1.26 50 16 113 97 88.00 2.47 51 16 116 100 87.97 2.45 52 17 20 3 484.14 1.48 53 17 21 4 435.60 1.23 54 17 24 7 393.59 3.50 55 17 109 92 88.11 2.66 56 17 113 96 94.22 0.42 57 18 21 3 486.89 0.71 58 20 23 3 470.66 0.92 59 20 24 4 463.24 2.10 60 21 24 3 464.99 1.23 61 21 25 4 454.29 2.38 62 21 63 42 101.99 1.43 63 22 25 3 462.45 2.27 64 22 26 4 454.28 2.39 65 22 59 37 106.25 0.48 66 22 60 38 102.21 1.39 67 22 63 41 102.21 1.40 68 23 26 3 481.24 5.01 69 23 27 4 465.16 3.02 70 24 27 3 481.23 5.01 71 24 28 4 463.43 2.10 72 24 108 84 126.69 0.80 73 24 109 85 132.25 2.12 74 24 112 88 139.52 0.10 75 24 113 89 141.35 0.82 76 25 28 3 471.67 0.24 77 25 29 4 467.10 2.05 78 25 59 34 120.73 0.45 79 25 63 38 118.96 0.35 80 26 29 3 470.75 2.66 81 26 30 4 465.31 1.16 82 26 55 29 137.35 1.24 83 26 56 30 130.97 4.44 84 26 59 33 123.51 0.78 85 27 30 3 465.30 1.15 86 27 31 4 465.29 1.15 87 27 108 81 141.70 0.88 88 27 112 85 141.87 0.84 89 28 31 3 464.56 0.79 90 28 32 4 471.81 2.85 91 28 101 73 141.56 0.84 92 28 104 76 141.63 0.87 93 28 105 77 141.62 0.86 94 28 108 80 141.81 0.83 95 29 32 3 475.41 1.05 96 29 33 4 474.38 1.57 97 29 55 26 141.91 0.83 98 29 58 29 141.78 0.84 99 29 59 30 141.75 0.85 100 29 101 72 141.63 0.86 101 30 33 3 481.62 2.06 102 30 34 4 466.38 2.43 103 30 50 20 142.32 0.87 104 31 35 4 450.75 3.39 105 31 104 73 142.09 0.88 106 31 107 76 142.12 0.86 107 31 108 77 142.12 0.86 108 32 35 3 472.81 2.03 109 32 36 4 457.17 0.88 110 32 39 7 363.99 1.18 111 32 101 69 142.03 0.88 112 32 104 72 142.11 0.87 113 33 36 3 479.35 0.87 114 33 37 4 443.65 5.88 115 33 39 6 345.19 8.23 116 33 40 7 324.31 10.38 117 33 43 10 296.04 2.77 118 33 48 15 142.40 0.84 119 34 37 3 484.63 1.77 120 36 39 3 493.45 4.57 121 36 100 64 142.18 0.86 122 36 103 67 142.28 0.84 123 36 104 68 142.30 0.85 124 37 40 3 480.70 0.27 125 38 41 3 481.80 0.73 126 39 42 3 486.06 0.97 127 39 43 4 476.86 0.35 128 39 97 58 142.19 0.85 129 39 100 61 142.31 0.83 130 40 43 3 476.44 0.56 131 40 44 4 472.15 1.35 132 40 48 8 253.79 4.37 133 41 44 3 496.03 2.68 134 42 92 50 142.19 0.75 135 42 93 51 142.17 0.74 136 42 94 52 142.34 0.81 137 42 97 55 142.34 0.81 138 43 46 3 479.62 1.90 139 43 48 5 434.92 3.55 140 43 58 15 238.38 0.52 141 45 54 9 248.35 1.44 142 46 54 8 248.30 1.45 143 46 58 12 248.30 1.45 144 47 52 5 248.39 1.45 145 47 54 7 248.36 1.44 146 47 55 8 248.36 1.44 147 48 55 7 248.35 1.44 148 49 52 3 477.72 0.00 149 52 55 3 475.32 0.19 150 52 56 4 463.73 5.83 151 53 56 3 472.00 1.70 152 53 57 4 473.51 0.94 153 54 57 3 482.67 3.62 154 54 58 4 474.28 0.61 155 55 58 3 474.29 0.60 156 55 59 4 474.29 0.60 157 56 59 3 475.38 1.16 158 56 60 4 474.31 0.61 159 57 60 3 474.31 0.62 160 57 61 4 474.30 0.62 161 58 61 3 474.29 0.62 162 58 62 4 474.28 0.62 163 59 62 3 474.52 0.52 164 59 63 4 465.19 3.28 165 60 63 3 473.66 0.95 166 60 64 4 465.26 3.24 167 61 64 3 480.18 2.83 168 61 65 4 465.25 3.23 169 62 65 3 480.05 1.96 170 62 66 4 467.45 4.33 171 63 66 3 477.43 0.65 172 63 67 4 467.45 4.33 173 64 67 3 464.94 5.60 174 64 68 4 459.40 2.98 175 65 68 3 459.33 3.01 176 65 69 4 459.33 3.02 177 65 80 15 154.52 1.71 178 65 83 18 154.49 1.71 179 66 69 3 468.44 2.71 180 66 70 4 464.25 0.59 181 66 105 39 168.91 0.74 182 66 128 62 179.40 4.81 183 66 129 63 170.53 0.42 184 66 132 66 159.80 0.93 185 67 70 3 477.08 0.45 186 67 71 4 469.64 3.28 187 68 71 3 476.83 0.31 188 68 72 4 469.64 3.28 189 69 72 3 477.73 0.76 190 69 73 4 465.63 5.28 191 69 76 7 281.89 0.67 192 69 80 11 163.74 2.89 193 69 128 59 182.22 3.45 194 69 132 63 168.99 0.28 195 70 73 3 477.10 0.45 196 70 128 58 182.22 3.45 197 72 75 3 479.03 3.52 198 72 76 4 441.27 1.96 199 72 79 7 261.37 1.17 200 73 76 3 482.31 1.88 201 75 78 3 480.12 1.86 202 75 79 4 421.54 4.21 203 76 79 3 460.34 3.05 204 76 80 4 421.43 4.26 205 76 128 52 199.44 4.89 206 76 131 55 198.30 4.38 207 76 132 56 198.28 4.39 208 76 135 59 196.06 3.29 209 77 135 58 198.27 4.38 210 78 81 3 453.38 7.71 211 80 83 3 483.19 1.16 212 80 84 4 480.67 2.42 213 80 132 52 200.00 4.75 214 80 135 55 199.84 4.69 215 80 136 56 199.94 4.74 216 81 84 3 480.69 2.42 217 81 85 4 485.27 0.13 218 81 139 58 199.78 4.71 219 82 85 3 487.67 0.84 220 82 86 4 485.26 0.13 221 83 86 3 487.43 0.96 222 83 87 4 476.84 4.33 223 83 136 53 200.06 4.73 224 84 87 3 480.68 2.16 225 84 88 4 462.20 2.98 226 84 135 51 200.06 4.73 227 84 136 52 200.06 4.73 228 84 138 54 200.04 4.73 229 84 139 55 199.86 4.70 230 85 88 3 460.40 1.09 231 85 89 4 416.42 10.51 232 85 90 5 418.94 11.77 233 85 139 54 199.86 4.70 234 86 90 4 395.56 23.46 235 86 91 5 345.62 23.95 236 87 91 4 331.21 18.88 237 87 92 5 311.38 16.70 238 87 93 6 302.47 12.26 239 87 98 11 267.30 3.37 240 87 136 49 200.11 4.74 241 88 92 4 311.33 16.68 242 88 139 51 199.94 4.74 243 88 140 52 199.82 4.72 244 93 97 4 473.50 3.12 245 93 98 5 473.50 3.12 246 94 97 3 482.03 2.04 247 95 98 3 478.83 0.45 248 95 99 4 478.51 0.61 249 95 137 42 200.97 4.59 250 96 99 3 478.83 0.45 251 96 100 4 473.51 3.10 252 97 100 3 471.62 2.85 253 97 101 4 465.99 0.76 254 98 101 3 478.18 2.19 255 98 102 4 465.99 0.76 256 98 133 35 201.04 4.62 257 98 136 38 201.06 4.62 258 99 102 3 476.16 0.08 259 99 103 4 470.24 2.88 260 100 103 3 474.17 0.91 261 100 104 4 474.17 0.91 262 101 104 3 471.88 2.22 263 101 105 4 467.06 0.45 264 102 105 3 474.62 2.31 265 102 106 4 464.63 1.66 266 102 129 27 203.93 3.35 267 102 133 31 203.83 3.30 268 103 106 3 468.94 2.41 269 103 107 4 464.63 1.66 270 104 107 3 466.04 0.96 271 104 108 4 464.61 1.67 272 105 108 3 465.66 1.69 273 105 109 4 460.68 0.29 274 105 129 24 205.38 3.84 275 106 109 3 469.68 3.70 276 106 110 4 466.69 0.33 277 106 117 11 206.80 3.91 278 106 122 16 205.98 3.76 279 106 125 19 205.87 3.81 280 106 126 20 205.86 3.81 281 106 129 23 205.78 3.83 282 107 110 3 475.77 2.30 283 107 111 4 470.10 0.54 284 108 111 3 466.70 2.24 285 108 112 4 465.63 2.77 286 109 112 3 472.80 5.34 287 109 113 4 458.09 0.99 288 109 125 16 206.01 3.75 289 110 117 7 216.18 2.82 290 113 116 3 477.32 0.82 291 113 117 4 459.22 1.32 292 114 117 3 481.69 0.72 293 115 118 3 522.32 1.08 294 116 121 5 452.34 1.69 295 117 121 4 452.79 3.46 296 117 122 5 422.73 16.48 297 117 125 8 392.44 1.93 298 118 121 3 465.62 0.21 299 118 122 4 453.37 3.22 300 119 122 3 460.34 1.16 301 119 123 4 453.32 3.20 302 120 123 3 464.36 0.85 303 120 124 4 462.94 1.55 304 121 124 3 464.81 0.62 305 121 125 4 458.25 0.59 306 122 126 4 458.25 0.58 307 123 126 3 473.75 3.94 308 123 127 4 462.63 1.62 309 124 127 3 465.35 0.27 310 124 128 4 462.62 1.62 311 125 128 3 472.37 0.56 312 125 129 4 469.63 0.14 313 126 129 3 478.23 3.81 314 126 130 4 465.66 1.85 315 127 130 3 476.88 3.14 316 127 131 4 465.04 1.53 317 128 131 3 476.88 3.14 318 128 132 4 465.75 1.17 319 129 132 3 477.62 2.76 320 129 133 4 464.56 1.77 321 130 133 3 467.31 1.01 322 130 134 4 460.47 0.29 323 131 134 3 462.25 1.19 324 131 135 4 460.45 0.29 325 132 135 3 473.60 2.85 326 132 136 4 458.08 0.88 327 133 137 4 451.07 5.25 328 134 137 3 469.00 1.88 329 134 138 4 453.93 3.81 330 135 138 3 472.71 2.66 331 137 140 3 487.82 1.55