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 5 451.26 7.64 2 2 73 71 30.11 0.42 3 2 127 125 26.25 0.94 4 2 128 126 26.25 0.94 5 3 6 3 470.42 1.94 6 3 7 4 469.79 1.62 7 4 7 3 478.39 1.64 8 4 8 4 469.79 1.62 9 5 8 3 472.42 0.96 10 5 9 4 470.44 1.95 11 6 9 3 480.53 2.49 12 6 10 4 471.04 2.25 13 6 124 118 49.88 0.02 14 6 127 121 49.27 0.33 15 7 10 3 478.69 1.56 16 7 11 4 471.63 4.22 17 7 73 66 49.92 0.03 18 7 74 67 49.93 0.02 19 8 11 3 482.49 4.55 20 8 12 4 471.64 4.21 21 9 12 3 477.43 1.33 22 9 13 4 471.66 4.21 23 9 121 112 50.84 0.04 24 9 124 115 50.79 0.06 25 10 13 3 484.29 1.39 26 10 14 4 471.66 4.21 27 10 70 60 50.70 0.07 28 10 124 114 50.79 0.06 29 10 125 115 50.68 0.09 30 10 128 118 50.68 0.09 31 11 14 3 476.73 1.66 32 11 15 4 471.64 4.21 33 11 70 59 50.70 0.07 34 12 15 3 478.23 1.64 35 12 16 4 476.36 1.06 36 13 16 3 483.32 1.34 37 13 17 4 476.35 1.06 38 13 125 112 50.90 0.03 39 14 17 3 479.56 0.54 40 14 18 4 470.43 1.90 41 14 67 53 50.88 0.03 42 14 70 56 50.88 0.03 43 15 18 3 473.85 0.39 44 16 113 97 94.44 1.02 45 17 20 3 494.76 0.62 46 17 21 4 464.93 6.92 47 17 24 7 400.87 1.76 48 17 109 92 93.95 1.26 49 17 113 96 94.46 1.03 50 18 21 3 504.94 3.25 51 20 23 3 480.76 0.60 52 20 24 4 475.40 3.29 53 21 24 3 480.69 0.64 54 21 25 4 465.93 1.45 55 21 63 42 102.41 2.42 56 22 25 3 470.00 0.58 57 22 26 4 468.10 2.22 58 22 59 37 106.11 0.58 59 22 60 38 103.93 1.66 60 22 63 41 103.92 1.66 61 23 26 3 472.61 0.04 62 23 27 4 468.12 2.21 63 24 27 3 477.45 2.26 64 24 28 4 472.75 0.10 65 24 108 84 122.66 0.19 66 24 109 85 125.91 0.10 67 24 112 88 137.36 0.72 68 25 28 3 491.35 2.05 69 25 29 4 482.73 2.27 70 25 59 34 121.87 0.52 71 25 105 80 122.75 0.24 72 26 29 3 484.20 1.53 73 26 30 4 482.74 2.27 74 26 55 29 132.15 0.46 75 26 56 30 134.66 0.80 76 26 59 33 122.09 0.42 77 27 30 3 484.56 1.35 78 27 31 4 475.36 1.43 79 27 108 81 137.83 0.89 80 27 112 85 138.66 0.55 81 28 31 3 475.65 1.58 82 28 32 4 475.35 1.44 83 28 101 73 137.71 0.89 84 28 104 76 137.75 0.88 85 28 105 77 137.71 0.89 86 28 108 80 137.89 0.86 87 29 32 3 478.59 1.08 88 29 33 4 472.63 2.79 89 29 55 26 138.79 0.45 90 29 58 29 138.16 0.72 91 29 59 30 137.94 0.83 92 29 62 33 137.93 0.83 93 29 101 72 137.80 0.88 94 30 33 3 475.98 1.43 95 30 34 4 472.62 2.80 96 30 50 20 139.19 0.53 97 31 34 3 477.67 0.08 98 31 35 4 469.43 1.21 99 31 104 73 138.69 0.55 100 31 107 76 138.85 0.56 101 31 108 77 138.94 0.55 102 31 111 80 139.19 0.56 103 32 35 3 483.22 1.23 104 32 36 4 454.24 1.40 105 32 39 7 226.33 40.14 106 32 101 69 138.69 0.55 107 32 104 72 138.80 0.58 108 33 37 4 427.48 11.99 109 33 39 6 150.24 0.95 110 33 40 7 147.16 0.59 111 33 43 10 142.16 1.11 112 33 48 15 139.38 0.55 113 33 55 22 139.25 0.54 114 36 39 3 492.43 3.70 115 36 100 64 138.79 0.59 116 36 103 67 139.12 0.53 117 36 104 68 139.13 0.53 118 37 40 3 490.14 1.07 119 38 41 3 504.55 3.04 120 38 97 59 138.92 0.55 121 39 42 3 499.31 5.66 122 39 43 4 494.81 3.41 123 39 97 58 138.84 0.58 124 40 43 3 498.51 1.56 125 40 48 8 143.59 2.29 126 41 44 3 489.57 2.91 127 42 91 49 138.82 0.58 128 42 92 50 138.86 0.57 129 42 93 51 138.86 0.57 130 42 94 52 139.00 0.50 131 42 97 55 139.09 0.53 132 43 46 3 479.80 0.46 133 43 48 5 413.08 16.89 134 43 58 15 139.77 0.70 135 46 54 8 140.33 0.69 136 46 58 12 140.18 0.62 137 47 52 5 143.71 2.21 138 47 54 7 140.39 0.67 139 47 55 8 140.42 0.69 140 48 52 4 369.86 4.78 141 48 55 7 140.52 0.64 142 49 52 3 472.36 3.36 143 52 55 3 475.99 1.54 144 52 56 4 472.31 3.38 145 53 56 3 465.01 0.28 146 53 57 4 465.55 0.01 147 54 57 3 476.44 1.44 148 54 58 4 460.53 2.65 149 55 58 3 475.73 1.79 150 55 59 4 470.24 2.19 151 56 59 3 475.95 3.29 152 56 60 4 475.95 3.29 153 57 60 3 486.89 1.48 154 57 61 4 475.96 3.29 155 58 61 3 481.03 0.76 156 58 62 4 475.95 3.29 157 59 62 3 482.58 0.03 158 59 63 4 481.88 0.32 159 60 63 3 482.56 0.04 160 60 64 4 471.23 5.00 161 61 64 3 481.73 1.24 162 61 65 4 464.30 1.54 163 62 65 3 479.38 0.06 164 62 66 4 465.32 2.07 165 63 66 3 470.88 0.70 166 63 67 4 462.38 3.53 167 64 67 3 472.00 1.26 168 64 68 4 476.84 1.17 169 65 68 3 476.86 1.17 170 65 69 4 476.86 1.18 171 65 83 18 172.81 1.81 172 66 69 3 476.88 1.19 173 66 70 4 476.85 1.18 174 66 105 39 174.89 2.81 175 66 128 62 175.16 2.70 176 66 129 63 173.33 1.79 177 66 132 66 173.03 1.89 178 67 70 3 481.16 0.72 179 67 71 4 478.60 0.30 180 68 71 3 484.23 2.50 181 68 72 4 474.40 3.25 182 68 79 11 180.16 1.15 183 68 80 12 174.52 1.66 184 69 72 3 484.47 2.39 185 69 73 4 473.49 3.71 186 69 76 7 241.19 35.31 187 69 80 11 174.22 1.82 188 69 128 59 179.34 0.62 189 69 132 63 174.05 1.79 190 70 73 3 485.75 1.74 191 70 128 58 184.21 1.79 192 72 75 3 472.37 1.09 193 72 76 4 400.25 3.53 194 72 79 7 306.17 2.81 195 73 76 3 490.13 0.15 196 75 78 3 497.86 0.89 197 75 79 4 465.33 1.51 198 76 79 3 479.24 1.33 199 76 80 4 465.34 1.52 200 76 128 52 272.22 4.25 201 76 131 55 270.63 3.51 202 76 132 56 261.26 1.18 203 76 135 59 261.23 1.17 204 77 80 3 478.99 0.06 205 77 81 4 454.70 2.83 206 77 135 58 261.23 1.17 207 78 81 3 483.79 2.46 208 80 83 3 500.00 3.92 209 80 84 4 467.38 1.75 210 80 132 52 285.28 4.58 211 80 135 55 282.38 3.15 212 80 136 56 282.38 3.14 213 81 84 3 482.51 2.22 214 81 85 4 469.10 0.90 215 81 139 58 283.77 3.79 216 82 85 3 482.19 1.39 217 82 86 4 469.11 0.90 218 83 86 3 477.62 0.90 219 83 87 4 469.11 0.90 220 83 136 53 288.05 4.55 221 84 87 3 483.24 3.71 222 84 88 4 466.00 1.08 223 84 135 51 288.03 4.55 224 84 136 52 288.03 4.55 225 84 138 54 288.01 4.54 226 84 139 55 288.01 4.54 227 85 88 3 473.78 0.04 228 85 89 4 452.30 1.71 229 85 90 5 416.73 16.07 230 85 139 54 288.01 4.54 231 86 90 4 395.17 5.29 232 86 91 5 377.88 3.35 233 87 91 4 376.32 4.12 234 87 92 5 341.83 6.24 235 87 93 6 296.26 4.32 236 87 98 11 293.47 3.23 237 87 136 49 288.20 4.55 238 87 140 53 288.12 4.58 239 88 92 4 339.12 12.96 240 88 136 48 288.21 4.55 241 88 137 49 288.13 4.58 242 88 139 51 288.12 4.58 243 88 140 52 288.10 4.57 244 89 92 3 483.32 1.62 245 89 139 50 288.12 4.58 246 92 140 48 288.22 4.56 247 93 97 4 480.72 0.56 248 93 98 5 473.47 3.06 249 93 140 47 288.33 4.50 250 94 97 3 487.94 2.23 251 95 98 3 484.49 2.20 252 95 99 4 481.34 0.24 253 95 137 42 288.70 4.54 254 95 140 45 288.69 4.54 255 96 99 3 480.11 0.26 256 96 100 4 473.55 3.02 257 97 100 3 474.51 2.54 258 97 101 4 473.56 3.01 259 98 101 3 479.70 1.86 260 98 102 4 474.97 0.51 261 98 133 35 288.74 4.53 262 98 136 38 288.79 4.51 263 98 137 39 288.75 4.53 264 99 102 3 474.93 0.53 265 99 103 4 474.93 0.53 266 100 103 3 475.67 0.16 267 100 104 4 471.70 1.82 268 101 104 3 472.75 1.30 269 101 105 4 472.12 0.98 270 102 105 3 475.92 0.24 271 102 106 4 472.79 1.32 272 102 129 27 289.03 4.54 273 102 133 31 288.98 4.57 274 103 106 3 475.92 0.24 275 103 107 4 471.72 1.85 276 104 107 3 471.50 1.96 277 104 108 4 471.50 1.96 278 105 108 3 471.54 1.97 279 105 109 4 471.57 1.92 280 105 129 24 290.31 4.23 281 106 109 3 478.91 1.96 282 106 110 4 471.12 1.76 283 106 117 11 295.20 2.17 284 106 122 16 290.54 4.27 285 106 125 19 290.43 4.26 286 106 126 20 290.37 4.25 287 106 129 23 290.37 4.25 288 107 110 3 471.90 1.78 289 107 111 4 471.15 1.78 290 108 111 3 482.19 0.59 291 108 112 4 476.31 0.81 292 109 112 3 479.43 1.72 293 109 113 4 468.70 2.84 294 109 117 8 313.37 10.87 295 109 125 16 290.61 4.29 296 110 113 3 476.95 0.48 297 110 114 4 456.92 3.04 298 110 117 7 312.99 11.06 299 113 116 3 492.22 2.44 300 113 117 4 460.18 7.05 301 114 117 3 492.22 2.44 302 115 118 3 515.61 1.53 303 116 121 5 463.54 3.89 304 117 121 4 463.54 3.90 305 117 122 5 463.24 4.04 306 118 121 3 473.11 0.89 307 118 122 4 472.51 0.58 308 119 122 3 478.78 3.69 309 119 123 4 472.54 0.57 310 120 123 3 477.05 2.82 311 120 124 4 472.54 0.57 312 121 124 3 484.38 0.18 313 121 125 4 472.53 0.57 314 122 125 3 484.38 0.17 315 122 126 4 467.56 1.91 316 123 126 3 484.38 0.18 317 123 127 4 475.00 4.50 318 124 127 3 483.60 0.20 319 124 128 4 475.66 1.04 320 125 128 3 484.14 0.48 321 125 129 4 478.37 2.41 322 126 129 3 484.32 0.17 323 126 130 4 478.34 2.42 324 127 130 3 483.59 0.20 325 127 131 4 478.34 2.42 326 128 131 3 478.37 2.41 327 128 132 4 478.34 2.43 328 129 132 3 479.31 1.79 329 129 133 4 470.60 0.33 330 130 133 3 471.67 0.86 331 130 134 4 470.60 0.33 332 131 134 3 471.81 0.80 333 131 135 4 470.60 0.33 334 132 135 3 493.79 4.95 335 132 136 4 470.60 0.33 336 133 136 3 480.36 1.77 337 133 137 4 465.68 1.83 338 134 137 3 487.10 0.27 339 134 138 4 461.37 0.12 340 134 141 7 391.89 2.79 341 135 138 3 465.89 2.64 342 137 140 3 486.76 1.69 343 137 141 4 476.31 0.31 344 138 141 3 478.62 1.48