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 73 71 19.42 0.06 2 2 76 74 17.81 0.07 3 2 127 125 16.24 1.24 4 2 128 126 16.62 0.70 5 2 131 129 15.89 0.99 6 3 6 3 460.22 2.49 7 3 7 4 445.94 5.89 8 4 7 3 466.88 0.94 9 4 8 4 458.25 0.39 10 5 8 3 458.25 0.39 11 5 9 4 458.21 0.42 12 6 9 3 464.10 1.25 13 6 10 4 461.93 1.44 14 6 124 118 37.84 0.53 15 6 127 121 37.21 0.22 16 7 10 3 465.34 0.01 17 7 11 4 461.94 1.44 18 7 73 66 37.94 0.62 19 7 74 67 37.95 0.62 20 8 11 3 464.54 0.15 21 8 12 4 473.30 4.23 22 9 12 3 473.30 4.24 23 9 13 4 473.30 4.24 24 9 120 111 40.73 0.32 25 9 121 112 39.90 0.07 26 9 124 115 39.04 0.34 27 10 13 3 474.57 3.60 28 10 14 4 462.48 1.33 29 10 70 60 39.01 0.36 30 10 124 114 39.09 0.33 31 10 125 115 39.08 0.33 32 10 128 118 38.99 0.36 33 11 14 3 462.48 1.33 34 11 15 4 462.31 1.41 35 11 70 59 39.12 0.29 36 12 15 3 468.97 0.61 37 12 16 4 457.87 0.08 38 13 16 3 466.81 0.84 39 13 17 4 463.97 0.88 40 13 113 100 73.94 1.56 41 13 121 108 48.90 1.00 42 13 125 112 39.99 0.06 43 14 17 3 471.44 3.96 44 14 18 4 460.75 1.36 45 14 67 53 39.98 0.05 46 15 18 3 465.83 0.87 47 16 113 97 82.95 1.28 48 16 116 100 82.47 1.50 49 17 20 3 476.97 1.26 50 17 21 4 423.26 9.38 51 17 24 7 364.79 2.00 52 17 109 92 82.67 1.26 53 17 113 96 87.39 0.71 54 18 21 3 489.47 2.00 55 20 23 3 468.53 1.66 56 20 24 4 458.17 1.16 57 21 24 3 459.86 0.32 58 21 25 4 459.86 0.32 59 21 63 42 91.76 0.77 60 22 25 3 459.99 0.38 61 22 26 4 459.91 0.34 62 22 59 37 122.84 10.76 63 22 60 38 119.34 12.51 64 22 63 41 93.31 0.00 65 23 26 3 464.55 0.09 66 23 27 4 459.90 0.34 67 24 27 3 461.85 0.64 68 24 28 4 461.87 0.62 69 24 108 84 124.01 8.23 70 24 112 88 131.13 1.64 71 25 28 3 463.74 1.49 72 25 29 4 462.07 0.53 73 25 59 34 126.12 9.43 74 26 29 3 465.19 1.04 75 26 30 4 458.95 1.04 76 26 55 29 141.74 1.77 77 26 56 30 141.34 1.95 78 26 59 33 137.78 3.60 79 27 30 3 463.46 0.04 80 27 31 4 459.02 1.07 81 27 108 81 139.52 0.59 82 27 112 85 139.28 0.23 83 28 31 3 462.27 0.55 84 28 32 4 459.93 0.64 85 28 101 73 139.66 0.69 86 28 104 76 139.55 0.62 87 28 105 77 139.55 0.62 88 28 108 80 139.56 0.61 89 29 32 3 461.09 1.23 90 29 33 4 462.44 0.62 91 29 55 26 146.96 4.01 92 29 58 29 141.95 1.76 93 29 59 30 141.91 1.76 94 29 62 33 141.88 1.77 95 29 101 72 139.68 0.68 96 30 33 3 471.15 3.73 97 30 34 4 462.44 0.61 98 30 50 20 157.95 9.29 99 31 34 3 467.02 0.14 100 31 35 4 459.09 1.06 101 31 104 73 139.92 0.50 102 31 107 76 140.08 0.41 103 31 108 77 140.08 0.40 104 31 111 80 140.15 0.37 105 32 35 3 462.44 0.61 106 32 36 4 449.88 3.54 107 32 39 7 264.32 3.50 108 32 43 11 258.60 0.63 109 32 100 68 140.00 0.54 110 32 101 69 139.99 0.54 111 32 104 72 140.07 0.43 112 33 37 4 370.17 5.28 113 33 39 6 307.94 16.55 114 33 40 7 253.73 3.06 115 33 43 10 253.72 3.06 116 33 48 15 163.78 12.05 117 33 55 22 158.03 9.29 118 36 39 3 487.37 0.41 119 36 100 64 140.69 0.81 120 36 103 67 140.81 0.74 121 36 104 68 140.81 0.73 122 37 40 3 487.38 0.40 123 38 41 3 492.10 0.78 124 39 42 3 492.23 0.71 125 39 43 4 478.03 0.52 126 39 97 58 140.70 0.84 127 39 100 61 140.84 0.76 128 40 43 3 478.01 0.51 129 40 48 8 248.19 11.60 130 41 44 3 478.00 0.52 131 42 91 49 141.36 1.10 132 42 92 50 141.38 1.10 133 42 93 51 141.38 1.09 134 42 94 52 141.51 1.07 135 42 97 55 141.47 1.04 136 43 46 3 482.24 3.60 137 43 48 5 408.91 18.98 138 43 58 15 177.04 18.56 139 46 54 8 239.31 3.85 140 46 58 12 185.87 22.84 141 47 52 5 274.03 2.77 142 47 54 7 241.06 4.03 143 47 55 8 243.54 5.25 144 48 52 4 429.10 0.86 145 48 55 7 252.94 0.56 146 49 52 3 465.66 2.69 147 51 56 5 443.20 4.55 148 52 55 3 460.78 4.22 149 52 56 4 451.85 0.37 150 53 56 3 451.88 0.35 151 53 57 4 451.84 0.38 152 54 57 3 461.22 0.32 153 54 58 4 457.20 2.31 154 55 58 3 462.12 0.77 155 55 59 4 457.20 2.31 156 56 59 3 465.78 1.06 157 56 60 4 458.12 2.77 158 57 60 3 477.42 6.88 159 57 61 4 458.10 2.77 160 58 61 3 465.73 1.03 161 58 62 4 457.03 2.39 162 59 62 3 458.94 1.43 163 59 63 4 457.01 2.39 164 60 63 3 461.30 0.33 165 60 64 4 457.11 2.46 166 61 64 3 473.95 4.42 167 61 65 4 461.15 0.54 168 62 65 3 462.99 1.46 169 62 66 4 458.55 1.84 170 62 101 39 143.18 0.54 171 63 66 3 463.99 0.58 172 63 67 4 458.60 1.82 173 64 67 3 465.95 0.41 174 64 68 4 458.60 1.82 175 65 68 3 462.55 0.15 176 65 69 4 458.61 1.82 177 65 83 18 150.97 0.76 178 66 69 3 465.62 1.68 179 66 70 4 458.61 1.82 180 66 105 39 152.26 5.11 181 66 128 62 149.65 6.38 182 66 129 63 149.29 6.52 183 66 132 66 142.71 3.44 184 67 70 3 462.78 3.49 185 67 71 4 447.41 3.76 186 68 71 3 466.43 1.67 187 68 72 4 450.83 5.47 188 68 79 11 175.35 12.91 189 69 72 3 468.21 3.21 190 69 73 4 440.98 3.74 191 69 76 7 257.27 3.18 192 69 80 11 175.07 12.30 193 69 128 59 156.26 9.65 194 69 132 63 144.62 4.29 195 70 73 3 454.90 10.12 196 70 128 58 161.57 12.30 197 72 75 3 467.16 4.00 198 72 76 4 425.61 3.33 199 72 79 7 310.69 5.84 200 73 76 3 471.66 0.86 201 75 78 3 475.33 1.56 202 75 79 4 446.61 1.99 203 76 79 3 467.09 4.33 204 76 80 4 437.66 2.45 205 76 128 52 184.12 23.33 206 76 131 55 183.63 23.37 207 76 132 56 183.48 23.29 208 76 135 59 183.44 23.30 209 77 80 3 471.09 1.96 210 77 81 4 435.94 3.33 211 77 135 58 183.05 23.48 212 78 81 3 459.93 6.23 213 80 83 3 469.93 2.43 214 80 84 4 462.87 5.96 215 80 132 52 183.47 23.69 216 80 135 55 183.38 23.71 217 80 136 56 183.37 23.73 218 81 84 3 470.97 1.92 219 81 85 4 462.88 5.96 220 81 139 58 182.03 24.38 221 82 85 3 471.00 1.93 222 82 86 4 470.54 2.15 223 83 86 3 470.89 2.33 224 83 87 4 470.56 2.17 225 83 136 53 182.31 24.30 226 84 87 3 476.90 0.67 227 84 88 4 469.14 2.88 228 84 135 51 182.37 24.27 229 84 136 52 181.65 24.62 230 84 139 55 178.94 25.91 231 85 88 3 472.85 1.17 232 85 89 4 462.87 6.01 233 85 139 54 178.96 25.91 234 86 89 3 472.37 1.28 235 86 90 4 436.81 8.87 236 86 91 5 394.37 4.98 237 87 91 4 383.68 8.07 238 87 92 5 371.97 2.27 239 87 93 6 353.29 11.60 240 87 98 11 268.63 8.59 241 88 92 4 353.34 11.58 242 88 139 51 177.72 26.57 243 88 140 52 177.65 26.57 244 89 92 3 470.47 0.09 245 89 139 50 178.99 25.94 246 89 141 52 177.66 26.57 247 93 97 4 472.04 2.19 248 93 98 5 466.69 3.48 249 93 140 47 177.75 26.62 250 94 97 3 472.64 1.90 251 94 98 4 472.06 2.19 252 95 98 3 484.87 2.10 253 95 137 42 178.55 26.43 254 95 140 45 177.89 26.69 255 96 99 3 475.84 0.29 256 96 100 4 472.05 2.19 257 97 100 3 474.47 0.39 258 97 101 4 463.31 5.19 259 98 101 3 472.41 1.42 260 98 102 4 457.86 5.86 261 98 133 35 182.78 24.53 262 98 136 38 180.35 25.75 263 98 137 39 178.77 26.53 264 99 102 3 467.66 1.23 265 99 103 4 451.71 2.78 266 100 103 3 469.48 0.32 267 100 104 4 463.09 2.91 268 101 104 3 464.40 2.25 269 101 105 4 461.55 3.68 270 102 105 3 468.01 0.45 271 102 106 4 461.67 3.62 272 102 129 27 183.85 24.06 273 102 133 31 182.81 24.53 274 103 106 3 468.00 0.45 275 103 107 4 465.12 1.94 276 104 107 3 468.06 0.48 277 104 108 4 470.56 0.79 278 105 108 3 470.56 0.78 279 105 109 4 465.15 1.93 280 105 129 24 184.32 24.29 281 106 109 3 476.26 2.07 282 106 110 4 465.12 1.92 283 106 117 11 216.57 9.36 284 106 122 16 184.64 24.29 285 106 125 19 184.50 24.34 286 106 126 20 184.44 24.31 287 106 129 23 184.40 24.32 288 107 110 3 465.13 1.92 289 107 111 4 465.12 1.92 290 108 111 3 468.87 0.06 291 108 112 4 468.87 0.04 292 109 112 3 469.30 0.26 293 109 113 4 444.51 3.23 294 109 125 16 189.96 21.82 295 110 113 3 457.07 5.85 296 110 117 7 216.59 9.36 297 113 116 3 470.62 0.89 298 113 117 4 380.61 29.50 299 115 118 3 516.29 3.90 300 116 121 5 442.73 4.62 301 117 121 4 445.59 3.21 302 117 122 5 439.53 3.06 303 117 125 8 400.43 11.73 304 118 121 3 458.94 6.24 305 118 122 4 448.46 1.77 306 119 122 3 465.81 2.81 307 119 123 4 452.88 0.28 308 120 123 3 471.29 0.06 309 120 124 4 453.42 0.01 310 121 124 3 462.28 4.45 311 121 125 4 456.05 1.33 312 122 125 3 472.65 0.86 313 122 126 4 455.36 1.66 314 123 126 3 464.84 3.08 315 123 127 4 459.56 3.76 316 124 127 3 463.69 9.11 317 124 128 4 456.26 5.41 318 125 128 3 473.26 2.19 319 125 129 4 453.16 6.96 320 126 129 3 470.56 0.66 321 126 130 4 446.74 3.74 322 127 130 3 457.69 1.72 323 127 131 4 446.72 3.73 324 128 131 3 450.86 1.67 325 128 132 4 446.76 3.71 326 129 132 3 458.31 2.06 327 129 133 4 446.73 3.69 328 130 133 3 452.70 0.72 329 130 134 4 446.75 3.70 330 131 134 3 463.39 4.62 331 131 135 4 452.70 0.72 332 132 135 3 472.94 2.12 333 132 136 4 452.70 0.72 334 133 136 3 465.09 7.59 335 133 137 4 440.76 2.45 336 134 137 3 465.76 7.25 337 134 138 4 448.74 1.54 338 135 138 3 471.44 4.41 339 137 140 3 495.65 1.03