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 5 452.85 1.77 2 2 127 125 22.80 0.51 3 2 128 126 22.80 0.52 4 3 6 3 491.12 0.41 5 3 7 4 467.54 0.38 6 3 127 124 32.47 0.83 7 4 7 3 469.58 0.07 8 4 8 4 452.85 1.77 9 5 9 4 457.66 0.15 10 6 9 3 457.79 0.10 11 6 10 4 458.08 0.01 12 6 124 118 40.59 2.88 13 6 127 121 37.02 1.09 14 7 10 3 486.58 0.46 15 7 11 4 463.89 2.90 16 7 73 66 42.16 2.06 17 8 11 3 465.82 1.94 18 8 12 4 463.89 2.90 19 9 12 3 474.62 1.91 20 9 13 4 463.88 2.90 21 9 121 112 52.00 0.14 22 9 124 115 51.08 0.60 23 10 13 3 457.92 0.09 24 10 14 4 452.48 2.15 25 10 15 5 455.63 1.27 26 10 70 60 51.06 0.61 27 10 124 114 51.69 0.29 28 10 125 115 51.04 0.61 29 10 128 118 51.02 0.62 30 11 15 4 464.50 3.17 31 11 70 59 51.04 0.62 32 12 15 3 471.30 6.57 33 12 16 4 467.11 1.90 34 13 16 3 486.06 0.34 35 13 113 100 71.50 1.80 36 13 121 108 53.51 0.18 37 13 125 112 52.39 0.19 38 14 17 3 485.12 0.14 39 14 63 49 60.57 1.17 40 14 66 52 52.39 0.18 41 14 67 53 52.67 0.04 42 14 70 56 52.39 0.18 43 14 105 91 62.30 2.02 44 14 109 95 71.22 1.75 45 15 18 3 495.06 4.84 46 16 113 97 91.38 2.79 47 16 116 100 80.95 2.40 48 17 20 3 462.62 0.29 49 17 21 4 453.51 4.26 50 17 24 7 342.48 9.68 51 17 109 92 87.05 0.63 52 17 113 96 91.46 2.77 53 18 21 3 484.06 0.57 54 20 23 3 481.31 1.82 55 20 24 4 442.88 4.32 56 21 24 3 471.98 2.31 57 21 25 4 442.88 4.32 58 21 59 38 107.58 2.03 59 21 63 42 94.71 1.11 60 22 26 4 453.84 1.13 61 22 59 37 109.52 1.06 62 22 60 38 105.83 1.62 63 23 26 3 467.78 0.87 64 23 27 4 453.85 1.13 65 24 28 4 463.40 2.01 66 24 108 84 123.36 0.19 67 24 109 85 132.30 1.62 68 24 112 88 139.19 0.46 69 24 113 89 142.22 0.58 70 25 28 3 467.25 2.00 71 25 29 4 465.33 1.04 72 25 59 34 122.70 0.53 73 25 63 38 117.03 1.01 74 26 29 3 489.94 0.39 75 26 55 29 141.15 0.11 76 26 56 30 132.41 4.26 77 26 59 33 125.58 0.89 78 27 30 3 480.38 2.17 79 27 31 4 479.56 2.68 80 27 50 23 179.60 0.76 81 27 56 29 144.31 0.48 82 27 108 81 147.93 1.43 83 28 31 3 479.56 2.68 84 28 32 4 479.56 2.68 85 28 101 73 148.16 1.47 86 28 104 76 148.12 1.49 87 28 105 77 148.06 1.48 88 28 108 80 147.93 1.43 89 29 32 3 479.56 2.68 90 29 33 4 467.05 3.58 91 29 43 14 272.56 10.01 92 29 55 26 145.97 0.38 93 29 58 29 145.91 0.37 94 29 101 72 148.22 1.47 95 30 33 3 478.11 3.40 96 30 34 4 463.99 2.04 97 31 34 3 476.51 0.74 98 31 35 4 462.37 2.85 99 31 104 73 148.38 1.62 100 31 107 76 148.06 1.48 101 31 108 77 148.09 1.50 102 32 36 4 443.15 2.36 103 32 39 7 332.44 6.90 104 32 43 11 280.54 6.04 105 32 100 68 149.68 0.96 106 32 101 69 148.46 1.58 107 32 104 72 148.38 1.62 108 33 36 3 496.86 1.10 109 33 39 6 333.11 6.57 110 33 40 7 319.50 13.37 111 33 43 10 275.35 8.63 112 33 48 15 208.06 1.77 113 33 55 22 187.27 0.47 114 36 39 3 504.34 0.29 115 36 100 64 150.31 0.72 116 36 103 67 150.36 0.72 117 36 104 68 150.31 0.72 118 37 40 3 504.44 0.14 119 38 41 3 497.47 3.35 120 38 42 4 488.63 1.05 121 38 97 59 150.56 0.58 122 38 100 62 150.62 0.62 123 39 42 3 496.19 2.10 124 39 43 4 488.64 1.06 125 39 97 58 150.53 0.56 126 39 100 61 150.63 0.62 127 40 43 3 482.89 1.80 128 40 48 8 260.85 1.60 129 42 93 51 150.88 0.59 130 42 94 52 150.89 0.58 131 42 97 55 150.87 0.59 132 43 46 3 464.63 2.90 133 43 48 5 439.04 9.90 134 43 58 15 256.06 0.43 135 45 54 9 261.12 1.71 136 46 54 8 261.10 1.72 137 46 55 9 261.10 1.72 138 46 58 12 261.03 1.69 139 47 52 5 330.31 28.70 140 47 54 7 261.16 1.69 141 47 55 8 267.75 5.01 142 49 52 3 488.01 3.45 143 51 56 5 440.01 10.87 144 52 55 3 479.70 3.02 145 52 56 4 455.79 3.02 146 53 56 3 473.10 3.01 147 53 57 4 452.78 4.52 148 54 57 3 477.23 2.56 149 54 58 4 458.71 1.55 150 55 58 3 469.28 1.10 151 55 59 4 459.57 1.12 152 56 59 3 472.66 0.58 153 57 60 3 486.46 4.19 154 57 61 4 469.06 1.20 155 58 61 3 467.00 2.23 156 58 62 4 468.56 1.46 157 59 63 4 440.35 0.38 158 60 64 4 433.07 10.23 159 61 64 3 453.31 4.15 160 61 65 4 448.14 2.69 161 62 66 4 461.25 0.69 162 62 101 39 151.63 0.36 163 62 105 43 151.06 0.56 164 63 66 3 472.59 3.25 165 63 67 4 476.60 1.72 166 64 67 3 478.42 0.82 167 65 68 3 478.59 0.78 168 65 69 4 475.77 1.28 169 65 80 15 196.63 6.49 170 65 83 18 166.45 1.21 171 66 69 3 477.48 1.56 172 66 70 4 476.66 1.74 173 66 105 39 151.70 0.40 174 66 128 62 148.47 1.58 175 66 132 66 145.90 1.13 176 67 70 3 483.80 2.26 177 67 71 4 478.43 0.85 178 68 71 3 478.46 0.86 179 68 72 4 470.91 4.63 180 69 72 3 478.42 0.90 181 69 73 4 448.04 3.32 182 69 76 7 318.96 5.21 183 69 80 11 215.62 0.00 184 69 128 59 148.56 1.54 185 69 132 63 147.57 1.19 186 70 73 3 468.13 6.03 187 70 128 58 148.55 1.55 188 71 74 3 527.56 0.53 189 72 75 3 487.89 1.11 190 72 76 4 443.03 0.07 191 72 79 7 275.45 2.07 192 73 76 3 471.12 2.14 193 75 78 3 471.62 4.17 194 75 79 4 441.92 2.91 195 76 79 3 446.14 0.80 196 76 80 4 448.94 0.18 197 76 128 52 148.80 1.44 198 76 131 55 148.44 1.52 199 76 135 59 145.06 0.07 200 77 81 4 450.62 0.66 201 77 135 58 144.25 0.34 202 78 81 3 466.82 3.64 203 80 83 3 481.06 3.77 204 80 84 4 467.52 4.69 205 80 135 55 144.24 0.32 206 80 136 56 143.81 0.36 207 81 84 3 467.52 4.69 208 81 85 4 459.19 0.53 209 81 139 58 142.97 0.20 210 82 85 3 467.69 4.60 211 82 86 4 459.38 0.43 212 83 86 3 460.97 1.23 213 83 87 4 460.97 1.23 214 83 136 53 143.10 0.14 215 84 135 51 143.77 0.39 216 84 136 52 142.97 0.21 217 84 138 54 142.95 0.20 218 84 139 55 142.88 0.17 219 85 88 3 476.92 1.54 220 85 89 4 450.17 4.17 221 85 139 54 142.70 0.20 222 86 90 4 369.69 6.30 223 86 91 5 369.69 6.29 224 87 91 4 347.74 4.67 225 87 92 5 294.41 7.92 226 87 93 6 294.41 7.92 227 87 98 11 275.80 1.36 228 87 136 49 142.88 0.17 229 87 140 53 137.46 0.35 230 88 92 4 301.00 4.62 231 88 139 51 141.12 0.52 232 88 140 52 136.97 0.10 233 92 140 48 134.80 1.07 234 93 97 4 461.89 1.59 235 93 98 5 459.28 0.29 236 93 140 47 134.02 1.47 237 94 97 3 478.99 4.33 238 94 98 4 467.81 1.26 239 94 140 46 131.39 0.61 240 95 98 3 471.85 0.98 241 95 99 4 467.82 1.26 242 95 137 42 135.78 1.17 243 95 140 45 131.21 0.70 244 96 99 3 480.72 3.46 245 96 100 4 467.82 1.26 246 97 100 3 467.88 1.23 247 97 101 4 470.12 0.10 248 98 101 3 481.98 0.96 249 98 102 4 464.93 2.49 250 98 133 35 142.66 0.05 251 98 136 38 141.30 0.52 252 98 137 39 139.04 0.46 253 99 102 3 464.93 2.49 254 99 103 4 464.93 2.49 255 100 104 4 464.91 2.50 256 101 104 3 463.27 1.05 257 101 105 4 454.84 5.26 258 102 106 4 475.80 1.64 259 102 129 27 148.40 2.90 260 102 133 31 148.37 2.91 261 103 106 3 481.51 1.22 262 104 107 3 481.34 4.41 263 104 108 4 472.19 0.01 264 105 108 3 476.05 1.66 265 105 109 4 472.46 0.12 266 105 129 24 161.75 1.61 267 106 109 3 473.86 0.58 268 106 110 4 471.12 0.52 269 106 117 11 192.80 1.29 270 106 122 16 169.12 1.79 271 106 125 19 168.81 1.86 272 106 126 20 163.69 0.70 273 106 129 23 163.06 0.98 274 107 110 3 466.85 2.69 275 107 111 4 462.61 0.58 276 108 112 4 414.28 1.06 277 109 113 4 408.91 1.61 278 109 117 8 213.99 4.71 279 109 125 16 175.50 0.48 280 110 117 7 213.14 5.12 281 111 114 3 467.68 1.54 282 113 116 3 475.19 2.22 283 113 117 4 429.47 1.02 284 114 117 3 477.91 0.91 285 115 118 3 515.20 1.38 286 116 121 5 440.51 1.02 287 117 121 4 440.97 1.24 288 117 122 5 436.37 1.06 289 117 125 8 422.44 4.30 290 118 121 3 449.66 3.10 291 118 122 4 449.71 3.08 292 119 122 3 464.55 10.89 293 120 123 3 470.48 2.10 294 120 124 4 459.78 3.26 295 121 124 3 462.43 1.94 296 121 125 4 454.98 5.67 297 122 125 3 472.91 0.89 298 122 126 4 462.44 1.94 299 123 126 3 470.48 2.08 300 123 127 4 457.84 4.24 301 124 128 4 456.61 3.62 302 125 128 3 468.69 0.68 303 125 129 4 460.57 2.73 304 126 129 3 464.99 0.52 305 126 130 4 443.86 0.04 306 127 130 3 462.44 0.76 307 127 131 4 443.87 0.04 308 128 131 3 471.48 1.31 309 128 132 4 460.19 6.95 310 129 132 3 462.02 6.14 311 129 133 4 443.81 0.19 312 130 134 4 460.25 7.02 313 131 134 3 466.55 3.77 314 131 135 4 464.50 7.33 315 132 135 3 476.59 1.30 316 132 136 4 476.10 1.54 317 134 137 3 472.63 0.15 318 134 138 4 445.74 1.96 319 135 138 3 464.30 4.01 320 137 140 3 443.22 1.75