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 5 444.99 5.39 2 2 73 71 28.94 0.12 3 2 76 74 28.45 0.36 4 2 127 125 23.43 0.11 5 2 128 126 23.43 0.11 6 2 131 129 23.42 0.12 7 3 6 3 467.54 0.38 8 3 7 4 467.54 0.38 9 4 7 3 480.93 1.65 10 4 8 4 467.54 0.38 11 5 8 3 480.93 1.65 12 5 9 4 467.53 0.38 13 6 9 3 479.72 1.04 14 6 10 4 459.14 0.54 15 6 124 118 46.68 0.13 16 6 127 121 45.20 0.87 17 7 10 3 469.53 4.66 18 7 11 4 471.19 3.83 19 7 73 66 47.18 0.35 20 7 74 67 47.23 0.37 21 8 11 3 470.93 2.31 22 8 12 4 459.16 0.29 23 9 12 3 460.01 0.72 24 9 13 4 469.46 4.55 25 9 121 112 50.21 0.87 26 9 124 115 50.02 0.95 27 10 13 3 485.19 2.35 28 10 14 4 472.64 6.12 29 10 70 60 49.86 0.91 30 10 124 114 50.02 0.95 31 10 128 118 49.86 0.91 32 11 14 3 482.41 1.25 33 11 15 4 474.12 5.38 34 11 70 59 49.88 0.89 35 11 73 62 49.91 0.88 36 12 15 3 482.40 1.25 37 12 16 4 480.64 2.12 38 13 16 3 480.91 1.99 39 13 17 4 480.64 2.12 40 13 113 100 73.70 2.75 41 13 121 108 58.41 2.68 42 13 125 112 50.80 0.95 43 14 17 3 480.63 2.11 44 14 18 4 480.62 2.10 45 14 66 52 50.82 0.95 46 14 67 53 50.82 0.95 47 14 70 56 50.81 0.95 48 14 109 95 73.59 2.77 49 15 18 3 477.58 0.58 50 16 113 97 74.23 2.54 51 16 116 100 74.14 2.56 52 17 20 3 488.03 0.12 53 17 21 4 438.43 4.12 54 17 24 7 403.85 6.68 55 17 109 92 74.19 2.52 56 18 21 3 492.70 2.92 57 20 23 3 481.31 1.82 58 20 24 4 463.01 3.20 59 21 24 3 475.75 0.96 60 21 25 4 470.74 0.61 61 21 63 42 95.83 0.58 62 22 25 3 486.73 2.44 63 22 26 4 470.74 0.60 64 22 60 38 97.95 0.47 65 22 63 41 101.18 1.16 66 23 26 3 489.08 1.27 67 23 27 4 468.50 0.51 68 24 27 3 476.43 4.25 69 24 28 4 465.38 1.05 70 24 108 84 120.22 0.33 71 24 109 85 124.37 1.58 72 24 112 88 132.16 1.07 73 25 28 3 465.37 1.06 74 25 29 4 465.37 1.06 75 25 59 34 117.29 1.12 76 25 63 38 117.27 1.12 77 26 29 3 477.72 3.60 78 26 30 4 461.75 2.43 79 26 55 29 129.45 0.26 80 26 56 30 129.12 0.42 81 26 59 33 117.92 1.43 82 27 30 3 471.44 1.40 83 27 31 4 462.75 1.92 84 27 108 81 132.77 0.96 85 27 112 85 133.75 0.93 86 28 31 3 477.45 1.61 87 28 32 4 474.53 0.15 88 28 101 73 132.72 0.96 89 28 104 76 132.74 0.96 90 28 105 77 132.71 0.96 91 28 108 80 133.06 0.91 92 29 32 3 474.53 0.15 93 29 33 4 474.53 0.15 94 29 55 26 132.87 1.01 95 29 58 29 132.78 0.96 96 29 59 30 132.72 0.97 97 29 101 72 132.77 0.96 98 30 33 3 478.36 2.08 99 30 34 4 473.06 0.89 100 30 50 20 133.86 1.06 101 31 34 3 484.68 1.08 102 31 35 4 470.49 2.17 103 31 104 73 133.77 0.97 104 31 107 76 133.84 0.97 105 31 108 77 133.84 0.98 106 31 111 80 134.03 0.98 107 32 35 3 482.99 0.24 108 32 36 4 448.68 8.73 109 32 39 7 304.47 0.65 110 32 43 11 292.57 0.09 111 32 101 69 133.77 0.97 112 32 104 72 133.81 0.97 113 33 37 4 424.06 2.84 114 33 39 6 318.54 7.75 115 33 40 7 292.56 0.09 116 33 43 10 289.91 1.24 117 33 48 15 134.06 1.05 118 33 55 22 133.94 1.04 119 34 37 3 492.65 1.00 120 36 39 3 495.73 4.01 121 36 100 64 133.82 0.97 122 36 104 68 133.96 0.99 123 37 40 3 488.88 0.91 124 38 41 3 495.62 4.27 125 39 42 3 492.44 0.83 126 39 97 58 133.79 0.97 127 39 100 61 133.90 0.96 128 40 43 3 483.38 1.55 129 40 48 8 189.88 26.79 130 41 44 3 494.00 1.50 131 42 92 50 133.79 0.98 132 42 93 51 133.75 0.96 133 42 94 52 133.81 0.97 134 42 97 55 134.01 0.98 135 43 46 3 478.10 0.99 136 43 48 5 428.38 15.23 137 43 58 15 175.49 19.62 138 45 54 9 189.66 26.16 139 46 54 8 189.65 26.14 140 46 58 12 189.59 26.16 141 47 52 5 285.60 3.65 142 47 54 7 189.68 26.16 143 47 55 8 285.59 3.64 144 48 55 7 285.60 3.64 145 49 52 3 481.79 1.32 146 51 56 5 454.85 3.50 147 52 55 3 481.49 1.80 148 52 56 4 475.40 1.86 149 53 56 3 476.76 1.18 150 53 57 4 461.22 1.80 151 54 57 3 469.69 1.01 152 54 58 4 467.46 0.11 153 55 58 3 480.57 0.73 154 55 59 4 467.53 0.07 155 56 59 3 476.75 2.65 156 56 60 4 467.70 0.01 157 57 60 3 486.46 4.19 158 57 61 4 469.60 0.93 159 58 61 3 472.64 0.59 160 58 62 4 464.67 1.54 161 59 62 3 482.34 6.25 162 59 63 4 469.18 3.81 163 60 63 3 472.17 2.32 164 60 64 4 467.57 0.18 165 61 64 3 482.48 2.83 166 61 65 4 467.59 0.17 167 62 65 3 482.36 2.90 168 62 66 4 467.59 0.17 169 62 101 39 152.38 0.93 170 63 66 3 478.22 4.97 171 63 67 4 467.56 0.15 172 64 67 3 470.42 1.58 173 64 68 4 468.74 4.80 174 65 68 3 476.42 0.96 175 65 69 4 469.66 5.26 176 65 80 15 145.78 2.41 177 65 83 18 145.71 2.43 178 66 69 3 478.47 0.86 179 66 70 4 469.66 5.26 180 66 105 39 160.47 1.15 181 66 129 63 159.30 1.06 182 66 132 66 152.97 0.92 183 67 70 3 478.47 0.86 184 67 71 4 478.46 0.86 185 68 71 3 478.48 0.86 186 68 72 4 478.46 0.86 187 68 79 11 197.57 20.21 188 69 72 3 476.73 1.72 189 69 73 4 467.41 6.37 190 69 76 7 288.07 8.47 191 69 80 11 181.84 15.35 192 69 128 59 200.50 7.63 193 69 132 63 160.02 1.44 194 70 73 3 466.12 0.45 195 70 128 58 200.55 7.70 196 72 75 3 473.09 0.18 197 72 76 4 441.81 6.02 198 72 79 7 283.45 3.51 199 73 76 3 482.03 1.83 200 75 78 3 504.09 4.62 201 75 79 4 455.58 2.28 202 76 79 3 452.17 3.13 203 76 80 4 448.62 4.90 204 76 128 52 225.48 9.45 205 76 131 55 224.50 9.42 206 76 132 56 224.46 9.43 207 76 135 59 224.44 9.43 208 77 81 4 424.87 9.53 209 77 135 58 224.44 9.42 210 78 81 3 459.02 7.54 211 80 83 3 475.75 1.86 212 80 84 4 449.72 3.51 213 80 132 52 226.22 9.58 214 80 136 56 226.02 9.62 215 81 84 3 474.45 1.23 216 81 85 4 450.62 3.96 217 81 139 58 225.94 9.65 218 82 85 3 472.52 2.19 219 82 86 4 452.15 4.72 220 83 86 3 462.72 1.26 221 83 87 4 451.62 4.99 222 83 136 53 226.24 9.58 223 84 88 4 451.67 3.45 224 84 135 51 226.23 9.60 225 84 136 52 226.22 9.59 226 84 139 55 226.18 9.61 227 85 88 3 459.32 7.28 228 85 89 4 442.77 2.34 229 85 139 54 226.15 9.60 230 86 90 4 354.31 9.97 231 86 91 5 310.94 7.05 232 87 91 4 296.41 3.54 233 87 92 5 288.08 7.67 234 87 93 6 275.94 2.33 235 87 98 11 275.56 2.34 236 87 140 53 226.18 9.61 237 88 92 4 277.87 2.56 238 88 139 51 226.19 9.60 239 88 140 52 226.16 9.61 240 89 92 3 482.43 2.46 241 89 139 50 226.27 9.58 242 93 97 4 481.67 2.98 243 93 98 5 455.44 0.86 244 93 140 47 226.32 9.57 245 94 97 3 489.04 0.20 246 95 98 3 485.59 1.03 247 95 137 42 227.35 9.46 248 95 140 45 226.47 9.54 249 96 99 3 491.85 2.10 250 96 100 4 481.66 2.99 251 97 100 3 478.88 6.00 252 97 101 4 469.66 1.38 253 98 101 3 473.95 0.76 254 98 102 4 473.89 0.73 255 98 133 35 227.62 9.50 256 98 136 38 227.73 9.51 257 98 137 39 227.66 9.52 258 98 140 42 227.62 9.55 259 99 102 3 473.95 0.77 260 99 103 4 473.89 0.73 261 100 103 3 480.50 0.23 262 100 104 4 468.36 3.51 263 101 104 3 470.44 2.52 264 101 105 4 470.38 2.49 265 102 105 3 472.37 2.69 266 102 106 4 470.39 2.49 267 102 129 27 228.03 9.39 268 102 133 31 227.99 9.42 269 103 106 3 478.42 0.33 270 103 107 4 466.93 4.26 271 104 107 3 473.88 0.78 272 104 108 4 473.88 0.79 273 105 108 3 473.88 0.78 274 105 109 4 468.13 2.09 275 105 129 24 229.19 9.56 276 106 109 3 473.68 0.68 277 106 110 4 468.12 2.10 278 106 117 11 230.24 9.46 279 106 122 16 229.69 9.54 280 106 125 19 229.46 9.52 281 106 126 20 229.46 9.52 282 106 129 23 229.38 9.48 283 107 110 3 473.88 0.58 284 107 111 4 467.88 2.21 285 108 111 3 479.22 3.46 286 108 112 4 463.48 0.01 287 109 112 3 472.73 0.02 288 109 113 4 463.47 0.00 289 109 125 16 229.83 9.61 290 110 117 7 230.25 9.46 291 113 116 3 473.24 3.19 292 113 117 4 404.56 0.90 293 115 118 3 515.71 1.12 294 116 121 5 429.76 6.92 295 117 121 4 443.12 0.24 296 117 122 5 430.17 6.71 297 117 125 8 429.60 6.96 298 118 121 3 454.31 0.42 299 118 122 4 448.11 2.67 300 119 122 3 475.31 5.50 301 119 123 4 458.85 2.69 302 120 123 3 469.07 1.34 303 120 124 4 462.45 1.95 304 121 124 3 462.49 1.96 305 121 125 4 462.51 1.95 306 122 125 3 473.75 0.47 307 122 126 4 462.51 1.95 308 123 126 3 473.75 0.47 309 123 127 4 470.55 2.06 310 124 127 3 472.37 1.16 311 124 128 4 470.48 2.10 312 125 128 3 462.42 1.92 313 125 129 4 457.07 3.64 314 126 129 3 461.24 1.28 315 126 130 4 450.18 0.18 316 127 130 3 460.88 3.33 317 127 131 4 457.16 3.64 318 128 131 3 470.86 1.66 319 128 132 4 469.31 2.43 320 129 132 3 476.88 1.36 321 129 133 4 469.30 2.43 322 130 133 3 470.45 2.00 323 130 134 4 469.14 2.50 324 131 134 3 476.67 1.26 325 131 135 4 476.66 1.26 326 132 135 3 476.66 1.27 327 132 136 4 476.66 1.27 328 133 136 3 485.07 5.40 329 133 137 4 476.73 1.23 330 134 137 3 477.03 1.36 331 134 138 4 470.38 1.96 332 135 138 3 471.91 1.21 333 136 140 4 482.73 0.39 334 137 140 3 480.44 1.53