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 5 450.69 3.23 2 2 10 8 441.73 7.71 3 2 73 71 39.23 0.65 4 2 128 126 25.16 1.30 5 2 131 129 24.98 1.40 6 3 6 3 473.44 3.25 7 3 7 4 481.84 1.20 8 4 7 3 485.03 0.40 9 4 8 4 481.98 1.14 10 5 8 3 482.41 0.96 11 5 9 4 481.98 1.14 12 6 9 3 482.02 1.15 13 6 10 4 481.98 1.14 14 6 124 118 55.89 0.14 15 6 127 121 54.90 0.35 16 7 10 3 489.47 2.57 17 7 11 4 481.44 0.86 18 7 73 66 55.76 0.10 19 7 74 67 59.13 1.58 20 8 11 3 485.12 2.70 21 8 12 4 481.12 1.02 22 9 12 3 484.50 2.70 23 9 13 4 480.48 0.69 24 9 121 112 70.95 0.57 25 9 124 115 70.95 0.57 26 10 13 3 484.50 2.70 27 10 14 4 480.49 0.69 28 10 70 60 71.39 0.73 29 10 73 63 71.41 0.74 30 10 124 114 70.97 0.57 31 10 125 115 70.96 0.57 32 10 128 118 70.91 0.56 33 11 14 3 486.98 1.47 34 11 15 4 481.97 1.43 35 11 70 59 71.38 0.77 36 11 71 60 71.53 0.74 37 11 73 62 71.41 0.76 38 12 15 3 482.09 1.37 39 12 16 4 481.99 1.44 40 13 16 3 481.99 1.44 41 13 17 4 481.80 1.54 42 13 121 108 71.71 0.83 43 13 125 112 71.69 0.83 44 14 17 3 481.81 1.54 45 14 18 4 481.80 1.54 46 14 63 49 71.73 0.83 47 14 66 52 71.72 0.83 48 14 67 53 71.73 0.83 49 14 70 56 71.72 0.83 50 15 18 3 496.51 0.16 51 16 113 97 93.50 2.31 52 16 116 100 93.45 2.30 53 17 20 3 484.57 1.88 54 17 21 4 476.78 5.76 55 17 24 7 403.83 7.25 56 17 109 92 93.47 2.33 57 17 113 96 97.80 0.96 58 18 21 3 496.40 0.26 59 20 23 3 479.73 0.20 60 20 24 4 474.17 0.13 61 21 24 3 487.12 6.59 62 21 25 4 475.98 1.03 63 21 63 42 103.74 0.58 64 22 25 3 480.23 0.43 65 22 26 4 475.99 1.03 66 22 60 38 108.28 2.83 67 22 63 41 103.81 0.59 68 23 26 3 483.40 1.57 69 23 27 4 475.98 1.04 70 24 27 3 476.99 1.56 71 24 28 4 474.57 1.73 72 24 108 84 129.58 1.06 73 24 109 85 129.80 0.96 74 24 112 88 137.63 0.31 75 25 28 3 486.91 1.14 76 25 29 4 474.67 1.70 77 25 59 34 128.26 1.77 78 25 63 38 124.95 0.56 79 26 29 3 486.91 1.14 80 26 30 4 474.67 1.64 81 26 55 29 136.78 0.24 82 26 56 30 136.54 0.42 83 26 59 33 131.68 0.12 84 27 30 3 484.42 1.60 85 27 31 4 472.88 0.72 86 27 108 81 138.36 0.26 87 27 112 85 139.10 0.29 88 28 31 3 486.19 0.71 89 28 32 4 474.78 1.66 90 28 104 76 137.99 0.33 91 28 105 77 137.99 0.33 92 28 108 80 138.38 0.26 93 29 32 3 479.54 4.04 94 29 33 4 474.79 1.67 95 29 55 26 138.52 0.32 96 29 58 29 138.49 0.33 97 29 59 30 138.47 0.33 98 29 101 72 138.31 0.25 99 30 33 3 485.11 3.50 100 30 34 4 474.79 1.67 101 30 50 20 139.16 0.29 102 31 34 3 486.38 4.13 103 31 35 4 472.84 0.70 104 31 104 73 138.36 0.24 105 31 107 76 139.19 0.23 106 31 108 77 139.19 0.23 107 32 35 3 489.67 2.50 108 32 36 4 462.51 2.00 109 32 39 7 327.54 4.39 110 32 43 11 292.82 0.03 111 32 101 69 138.34 0.26 112 32 104 72 138.40 0.25 113 33 37 4 430.09 13.88 114 33 39 6 316.47 9.92 115 33 40 7 290.91 0.93 116 33 43 10 291.50 0.64 117 33 48 15 139.41 0.19 118 34 37 3 493.26 0.59 119 36 39 3 496.60 1.11 120 36 100 64 139.07 0.18 121 36 103 67 139.31 0.21 122 37 40 3 491.36 1.66 123 38 41 3 497.66 1.18 124 39 42 3 496.36 1.83 125 39 43 4 491.68 0.01 126 39 97 58 138.35 0.26 127 39 100 61 139.28 0.16 128 40 43 3 491.68 0.01 129 40 48 8 247.21 0.87 130 41 44 3 491.18 1.19 131 42 93 51 138.30 0.25 132 42 94 52 139.21 0.12 133 42 97 55 139.29 0.15 134 43 46 3 479.17 4.37 135 43 48 5 419.77 2.36 136 43 58 15 230.82 4.04 137 45 54 9 245.53 1.98 138 46 54 8 245.52 1.97 139 46 58 12 245.51 1.98 140 47 52 5 258.97 3.48 141 47 54 7 245.53 1.97 142 47 55 8 245.53 1.97 143 48 55 7 245.53 1.97 144 49 52 3 484.97 0.40 145 52 55 3 486.68 2.58 146 52 56 4 478.47 1.95 147 53 56 3 481.94 0.21 148 53 57 4 470.17 2.21 149 54 58 4 471.26 3.17 150 55 58 3 478.46 1.95 151 55 59 4 471.24 3.15 152 56 59 3 482.62 3.19 153 56 60 4 472.24 2.68 154 57 60 3 490.69 4.16 155 57 61 4 481.26 0.43 156 58 61 3 492.47 0.48 157 58 62 4 479.80 1.17 158 59 62 3 482.19 0.04 159 59 63 4 473.52 1.97 160 60 63 3 485.14 1.52 161 60 64 4 476.21 2.96 162 61 64 3 474.07 1.88 163 61 65 4 475.06 2.50 164 62 65 3 484.34 1.91 165 62 66 4 479.12 4.52 166 63 66 3 484.34 1.91 167 63 67 4 481.50 3.33 168 64 67 3 478.90 0.64 169 64 68 4 477.53 1.32 170 65 68 3 487.50 3.66 171 65 69 4 477.53 1.33 172 65 83 18 149.26 3.04 173 66 69 3 477.53 1.33 174 66 70 4 477.53 1.34 175 66 105 39 181.53 1.83 176 66 129 63 179.41 2.89 177 66 132 66 157.74 1.62 178 67 70 3 482.89 0.29 179 67 71 4 477.55 1.34 180 68 71 3 478.88 2.02 181 68 72 4 477.54 1.35 182 68 79 11 227.04 3.00 183 69 72 3 477.52 1.35 184 69 73 4 477.50 1.36 185 69 76 7 302.56 3.36 186 69 80 11 192.94 14.82 187 69 128 59 198.69 2.12 188 69 132 63 181.12 2.04 189 70 73 3 485.13 2.44 190 70 128 58 199.11 1.99 191 72 75 3 485.81 1.51 192 72 76 4 475.29 3.45 193 72 79 7 282.32 2.98 194 73 76 3 483.38 1.16 195 73 128 55 205.86 0.18 196 75 78 3 487.70 1.01 197 75 79 4 471.41 2.38 198 76 79 3 475.99 4.25 199 76 80 4 470.12 1.74 200 76 131 55 208.19 0.78 201 76 132 56 208.00 0.88 202 76 135 59 208.00 0.87 203 77 81 4 455.62 5.50 204 77 135 58 208.00 0.87 205 78 81 3 491.56 1.49 206 79 82 3 636.75 5.21 207 80 83 3 493.22 1.84 208 80 84 4 472.47 2.32 209 80 132 52 209.04 0.70 210 80 135 55 208.97 0.74 211 80 136 56 208.97 0.73 212 81 84 3 486.34 1.59 213 81 85 4 476.06 3.54 214 82 85 3 480.25 1.74 215 82 86 4 473.03 2.03 216 83 86 3 476.06 3.55 217 83 87 4 473.00 2.04 218 83 136 53 209.09 0.69 219 84 87 3 485.62 4.29 220 84 88 4 471.20 1.13 221 84 135 51 209.25 0.77 222 84 136 52 209.07 0.68 223 84 138 54 209.06 0.68 224 85 88 3 484.14 0.81 225 85 89 4 453.69 5.93 226 85 90 5 446.55 2.35 227 86 90 4 393.77 8.27 228 86 91 5 393.76 8.27 229 87 91 4 388.88 10.72 230 87 92 5 379.42 15.44 231 87 93 6 370.78 19.74 232 87 98 11 268.56 7.09 233 87 136 49 209.59 0.78 234 88 92 4 372.28 19.00 235 88 136 48 209.65 0.79 236 88 139 51 209.25 0.70 237 88 140 52 209.18 0.73 238 89 92 3 490.21 1.44 239 89 139 50 209.28 0.70 240 93 97 4 484.80 0.35 241 93 98 5 476.81 3.65 242 93 140 47 209.71 0.80 243 94 97 3 491.00 1.07 244 95 98 3 490.55 0.85 245 95 137 42 210.02 0.74 246 95 140 45 210.00 0.74 247 96 99 3 490.41 1.38 248 96 100 4 484.46 2.29 249 97 100 3 484.46 2.29 250 97 101 4 482.00 1.06 251 98 101 3 485.07 0.55 252 98 102 4 481.91 1.03 253 98 133 35 210.50 0.86 254 98 136 38 210.60 0.91 255 98 137 39 210.48 0.87 256 99 102 3 486.29 1.18 257 99 103 4 481.88 1.02 258 100 103 3 487.86 1.01 259 100 104 4 478.02 2.37 260 101 104 3 477.88 5.33 261 101 105 4 474.38 0.65 262 102 105 3 480.83 3.87 263 102 106 4 474.38 0.65 264 102 129 27 210.93 0.96 265 103 106 3 481.00 0.74 266 103 107 4 473.72 0.84 267 104 107 3 475.55 0.07 268 104 108 4 473.72 0.84 269 105 108 3 476.00 0.29 270 105 109 4 470.38 2.53 271 105 129 24 212.43 0.73 272 106 109 3 481.95 3.23 273 106 110 4 470.38 2.54 274 106 117 11 331.36 9.28 275 106 122 16 212.74 0.70 276 106 125 19 212.69 0.69 277 106 126 20 212.56 0.74 278 106 129 23 212.64 0.69 279 107 110 3 481.42 2.96 280 107 111 4 478.16 1.33 281 108 111 3 487.95 0.82 282 108 112 4 483.94 1.55 283 109 112 3 488.32 0.64 284 109 113 4 475.65 0.06 285 109 117 8 314.86 0.89 286 109 125 16 212.79 0.70 287 110 113 3 487.54 0.61 288 110 114 4 453.76 2.31 289 110 117 7 314.10 0.64 290 111 114 3 500.31 4.18 291 113 116 3 485.31 0.76 292 113 117 4 465.42 3.90 293 114 117 3 471.17 1.02 294 115 118 3 518.10 0.83 295 116 121 5 446.43 1.02 296 117 122 5 446.44 1.02 297 118 121 3 484.23 2.27 298 118 122 4 463.48 4.88 299 119 122 3 476.22 1.49 300 119 123 4 465.30 3.97 301 120 123 3 476.21 1.49 302 120 124 4 461.73 6.17 303 121 124 3 473.43 0.33 304 121 125 4 466.33 3.87 305 122 125 3 473.42 0.33 306 122 126 4 458.84 0.10 307 123 126 3 466.35 3.85 308 123 127 4 466.10 3.73 309 124 127 3 471.81 0.89 310 124 128 4 458.22 0.20 311 125 128 3 477.44 1.93 312 125 129 4 456.49 0.67 313 126 129 3 485.11 1.91 314 126 130 4 457.85 1.35 315 127 130 3 481.26 2.77 316 127 131 4 459.69 4.91 317 128 131 3 484.04 1.39 318 128 132 4 462.66 6.38 319 129 132 3 478.36 1.46 320 129 133 4 462.69 6.37 321 130 133 3 475.94 0.25 322 130 134 4 469.77 2.85 323 131 134 3 481.19 4.17 324 131 135 4 469.77 2.85 325 132 135 3 486.25 1.64 326 132 136 4 469.79 2.83 327 133 136 3 485.36 1.76 328 133 137 4 473.57 0.66 329 134 137 3 476.19 0.66 330 134 138 4 467.18 3.85 331 135 138 3 467.18 3.85 332 137 140 3 491.75 0.19 333 138 141 3 499.52 1.88