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 4 48 44 66.98 0.64 2 4 49 45 66.98 0.65 3 4 50 46 66.97 0.65 4 4 136 132 66.93 0.62 5 5 46 41 67.07 0.64 6 5 47 42 67.06 0.64 7 5 48 43 67.00 0.65 8 5 50 45 67.03 0.65 9 5 51 46 67.02 0.64 10 5 73 68 66.97 0.64 11 5 76 71 67.00 0.63 12 5 135 130 66.98 0.62 13 5 136 131 66.93 0.62 14 6 45 39 67.09 0.64 15 6 46 40 67.07 0.64 16 6 47 41 67.08 0.63 17 6 136 130 66.99 0.63 18 6 137 131 66.97 0.64 19 6 138 132 66.95 0.62 20 7 44 37 67.36 0.58 21 7 45 38 67.14 0.65 22 7 46 39 67.09 0.64 23 7 71 64 66.97 0.64 24 7 138 131 66.97 0.64 25 8 43 35 67.77 0.78 26 8 44 36 67.35 0.58 27 8 45 37 67.14 0.65 28 8 138 130 67.00 0.63 29 8 139 131 66.96 0.63 30 8 140 132 66.96 0.63 31 9 37 28 68.34 0.61 32 9 43 34 68.23 0.55 33 9 44 35 67.36 0.58 34 9 57 48 67.11 0.64 35 9 71 62 67.14 0.65 36 9 140 131 66.97 0.63 37 9 142 133 66.94 0.63 38 10 41 31 68.85 0.48 39 10 43 33 68.23 0.55 40 10 140 130 67.00 0.62 41 10 141 131 66.97 0.63 42 10 142 132 66.95 0.63 43 11 59 48 69.27 0.76 44 11 142 131 66.95 0.63 45 11 144 133 66.95 0.63 46 12 141 129 67.00 0.63 47 12 142 130 66.97 0.63 48 12 143 131 66.95 0.64 49 12 144 132 66.95 0.64 50 13 20 7 228.58 72.28 51 13 21 8 221.62 75.61 52 13 144 131 66.94 0.64 53 14 143 129 67.00 0.63 54 14 144 130 66.96 0.64 55 14 145 131 66.92 0.65 56 15 18 3 488.47 0.89 57 15 145 130 66.92 0.66 58 16 19 3 465.92 1.68 59 18 61 43 345.60 0.73 60 18 124 106 78.02 1.18 61 19 61 42 346.04 0.85 62 19 62 43 346.08 0.83 63 20 61 41 346.07 0.84 64 20 62 42 346.12 0.83 65 21 59 38 346.04 0.85 66 21 60 39 346.12 0.83 67 21 61 40 346.12 0.83 68 21 65 44 346.61 0.67 69 21 67 46 346.04 0.85 70 21 124 103 136.22 0.58 71 21 144 123 66.98 0.62 72 22 59 37 346.21 0.86 73 22 60 38 346.16 0.83 74 23 26 3 542.53 0.53 75 23 44 21 360.20 5.40 76 23 57 34 346.19 0.86 77 23 58 35 346.22 0.86 78 23 59 36 346.24 0.85 79 24 58 34 347.13 0.65 80 24 59 35 347.13 0.65 81 24 60 36 347.14 0.66 82 25 57 32 347.22 0.68 83 25 58 33 347.16 0.66 84 25 91 66 253.84 0.84 85 25 92 67 253.75 0.86 86 25 93 68 253.74 0.86 87 26 37 11 361.04 5.51 88 26 56 30 347.26 0.65 89 26 57 31 347.27 0.65 90 27 37 10 361.46 5.58 91 27 55 28 347.78 0.40 92 27 56 29 347.29 0.65 93 27 92 65 253.84 0.85 94 27 93 66 253.83 0.85 95 27 96 69 253.37 0.85 96 28 34 6 371.62 1.14 97 28 35 7 362.21 5.80 98 28 36 8 361.62 5.51 99 28 37 9 361.62 5.51 100 28 46 18 361.09 5.33 101 28 54 26 348.75 0.70 102 28 55 27 347.29 0.65 103 29 34 5 374.12 0.48 104 29 53 24 349.87 0.35 105 29 54 25 348.80 0.69 106 29 96 67 253.75 0.84 107 29 97 68 253.66 0.85 108 29 100 71 252.94 1.05 109 29 101 72 252.94 1.04 110 30 34 4 403.69 15.25 111 31 34 3 466.60 1.11 112 31 52 21 367.88 0.98 113 31 53 22 356.85 3.61 114 31 100 69 253.57 0.85 115 32 49 17 369.06 1.25 116 32 50 18 369.03 1.23 117 32 51 19 368.94 1.20 118 32 52 20 368.62 1.10 119 32 53 21 367.87 0.98 120 33 49 16 369.16 1.20 121 34 48 14 369.35 1.20 122 34 49 15 369.33 1.20 123 34 53 19 361.75 2.41 124 35 47 12 369.36 1.19 125 35 48 13 369.35 1.19 126 36 46 10 369.67 1.07 127 36 47 11 369.64 1.06 128 37 44 7 370.88 0.73 129 37 45 8 370.46 0.70 130 37 46 9 370.31 0.74 131 37 55 18 357.06 4.78 132 37 56 19 357.05 4.79 133 37 57 20 357.00 4.79 134 38 44 6 371.12 0.85 135 38 45 7 370.72 0.82 136 39 43 4 409.88 1.97 137 39 44 5 371.12 0.86 138 40 43 3 459.44 7.29 139 44 57 13 357.10 4.84 140 46 54 8 357.99 4.41 141 46 55 9 357.95 4.40 142 46 71 25 347.53 0.71 143 48 53 5 379.24 1.20 144 48 54 6 362.30 3.69 145 48 72 24 347.49 0.70 146 48 73 25 347.46 0.70 147 51 73 22 347.47 0.70 148 51 75 24 347.07 0.54 149 51 76 25 345.08 0.43 150 52 73 21 347.47 0.70 151 52 100 48 253.39 0.94 152 53 72 19 347.48 0.70 153 53 73 20 347.45 0.71 154 53 100 47 253.31 0.97 155 54 71 17 347.51 0.72 156 54 72 18 347.45 0.71 157 54 79 25 255.39 0.59 158 54 96 42 253.74 0.87 159 54 100 46 252.87 1.01 160 55 70 15 347.57 0.72 161 55 71 16 347.53 0.72 162 55 96 41 253.41 0.89 163 56 68 12 347.79 0.71 164 56 69 13 347.62 0.70 165 56 70 14 347.58 0.71 166 56 92 36 253.83 0.85 167 56 96 40 252.94 1.05 168 57 68 11 347.81 0.70 169 57 69 12 347.66 0.69 170 58 67 9 348.00 0.69 171 58 68 10 347.82 0.70 172 58 86 28 254.15 0.87 173 58 91 33 253.82 0.85 174 58 92 34 253.70 0.86 175 59 66 7 348.05 0.69 176 59 67 8 348.03 0.69 177 59 69 10 348.01 0.69 178 59 144 85 66.97 0.62 179 60 64 4 429.58 0.82 180 60 65 5 374.00 2.23 181 60 66 6 348.06 0.69 182 61 64 3 462.99 1.30 183 61 65 4 405.01 7.74 184 65 120 55 145.96 0.54 185 65 122 57 145.72 0.55 186 65 124 59 145.58 0.55 187 66 85 19 254.03 0.86 188 66 86 20 253.98 0.86 189 66 87 21 253.98 0.86 190 66 88 22 253.95 0.85 191 67 82 15 254.26 0.88 192 67 83 16 254.22 0.90 193 67 84 17 254.14 0.88 194 67 86 19 254.05 0.84 195 67 124 57 145.44 0.64 196 67 126 59 142.34 0.53 197 67 144 77 66.98 0.62 198 68 82 14 254.28 0.89 199 68 83 15 254.25 0.88 200 68 86 18 254.15 0.88 201 68 95 27 252.83 0.98 202 69 81 12 254.41 0.85 203 69 82 13 254.30 0.90 204 69 128 59 141.36 0.35 205 69 142 73 66.98 0.62 206 70 79 9 255.28 0.57 207 70 80 10 254.62 0.83 208 70 81 11 254.42 0.85 209 70 99 29 252.40 0.79 210 71 79 8 255.28 0.58 211 71 80 9 254.63 0.83 212 71 128 57 141.50 0.32 213 71 130 59 141.25 0.41 214 72 78 6 320.62 33.20 215 72 79 7 313.10 29.45 216 73 76 3 470.72 2.06 217 73 77 4 426.81 3.20 218 73 78 5 320.62 33.20 219 73 79 6 320.62 33.20 220 74 77 3 462.53 5.35 221 74 79 5 385.97 0.57 222 74 109 35 190.84 1.98 223 74 110 36 190.72 1.96 224 77 112 35 183.70 1.32 225 78 112 34 174.99 1.08 226 78 113 35 174.99 1.08 227 78 114 36 171.59 2.55 228 78 130 52 141.46 0.34 229 78 133 55 116.79 1.30 230 79 99 20 253.19 0.92 231 79 100 21 253.19 0.92 232 79 109 30 190.31 1.80 233 79 112 33 171.60 2.69 234 79 113 34 171.12 2.78 235 79 130 51 141.48 0.34 236 80 113 33 170.81 2.79 237 80 115 35 152.22 1.61 238 80 116 36 146.81 0.45 239 80 128 48 141.50 0.32 240 80 130 50 141.47 0.34 241 81 99 18 252.84 1.01 242 81 108 27 190.49 1.89 243 81 116 35 146.80 0.45 244 82 116 34 146.59 0.38 245 82 118 36 146.23 0.42 246 82 126 44 143.67 0.07 247 82 128 46 141.50 0.32 248 83 86 3 519.25 0.85 249 83 99 16 252.84 1.02 250 83 105 22 190.87 1.90 251 84 118 34 146.15 0.46 252 84 120 36 145.91 0.55 253 85 120 35 145.94 0.53 254 86 90 4 432.49 4.74 255 87 90 3 459.87 2.31 256 88 91 3 502.21 0.52 257 89 94 5 461.26 3.04 258 90 94 4 461.25 3.04 259 91 94 3 464.17 1.78 260 91 95 4 462.03 2.67 261 92 95 3 466.83 0.27 262 92 96 4 465.24 1.06 263 92 97 5 469.84 2.47 264 93 97 4 476.20 1.77 265 94 97 3 496.45 0.24 266 94 98 4 481.14 0.11 267 95 98 3 486.24 2.66 268 95 99 4 487.42 2.06 269 96 99 3 490.06 0.74 270 96 100 4 488.05 1.76 271 97 100 3 481.50 0.66 272 98 103 5 408.89 2.54 273 98 104 6 408.91 2.53 274 98 105 7 408.91 2.52 275 98 106 8 408.91 2.52 276 99 105 6 408.90 2.52 277 99 106 7 408.90 2.52 278 99 108 9 408.90 2.52 279 99 109 10 408.82 2.50 280 100 103 3 465.62 2.53 281 100 106 6 408.90 2.52 282 100 109 9 408.84 2.50 283 101 106 5 432.25 0.24 284 102 106 4 441.35 0.28 285 103 106 3 497.31 0.50 286 105 108 3 489.85 6.17 287 105 109 4 476.86 0.33 288 106 109 3 476.86 0.32 289 106 110 4 464.30 3.29 290 107 110 3 471.19 2.52 291 107 111 4 468.86 1.34 292 108 111 3 468.87 1.34 293 109 112 3 479.82 1.02 294 113 116 3 505.28 0.15 295 113 130 17 141.80 0.29 296 114 129 15 141.81 0.29 297 114 130 16 141.65 0.31 298 114 133 19 119.16 0.12 299 115 128 13 141.88 0.27 300 115 129 14 141.68 0.34 301 116 127 11 142.60 0.47 302 116 128 12 142.00 0.33 303 117 125 8 146.10 0.73 304 117 126 9 145.84 0.64 305 117 127 10 142.84 0.35 306 118 125 7 146.10 0.74 307 118 126 8 146.08 0.74 308 119 123 4 423.67 4.32 309 119 124 5 160.65 0.89 310 119 125 6 150.61 1.51 311 120 123 3 448.57 11.44 312 120 124 4 402.07 11.80 313 124 145 21 66.98 0.62 314 125 143 18 67.03 0.64 315 125 144 19 66.98 0.62 316 125 145 20 66.96 0.62 317 126 142 16 67.03 0.63 318 126 143 17 67.00 0.62 319 126 144 18 66.98 0.62 320 127 141 14 67.03 0.63 321 127 142 15 67.00 0.62 322 127 143 16 66.98 0.62 323 128 140 12 67.04 0.63 324 128 141 13 67.00 0.62 325 128 142 14 66.99 0.62 326 129 140 11 67.03 0.62 327 129 141 12 67.01 0.63 328 130 133 3 446.76 1.36 329 130 138 8 73.70 2.69 330 130 139 9 67.05 0.62 331 130 140 10 67.00 0.62 332 131 139 8 73.69 2.69 333 131 140 9 67.05 0.62 334 131 141 10 67.03 0.63 335 132 137 5 306.54 53.88 336 132 138 6 73.90 2.81 337 132 139 7 73.69 2.69