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 1 9 8 485.78 1.03 2 1 41 40 147.49 2.58 3 1 46 45 141.83 0.26 4 2 5 3 516.41 3.06 5 2 6 4 508.68 1.09 6 2 37 35 152.71 2.15 7 3 6 3 509.75 1.08 8 3 7 4 508.68 1.09 9 4 7 3 510.62 0.12 10 4 8 4 503.31 3.77 11 4 27 23 177.75 0.79 12 4 29 25 177.42 0.75 13 4 37 33 153.56 1.74 14 5 8 3 508.25 0.75 15 5 9 4 507.20 0.23 16 5 37 32 152.75 2.15 17 5 41 36 152.71 2.15 18 6 9 3 509.94 1.14 19 6 10 4 507.19 0.23 20 6 149 143 14.84 0.14 21 7 10 3 507.35 0.15 22 7 11 4 506.86 0.40 23 7 26 19 178.76 0.41 24 7 27 20 178.46 0.44 25 8 11 3 513.03 2.10 26 8 12 4 506.57 0.54 27 8 27 19 178.61 0.36 28 8 34 26 164.62 2.18 29 8 37 29 156.58 1.73 30 8 38 30 153.56 1.74 31 9 12 3 511.41 2.88 32 9 13 4 500.74 2.44 33 9 41 32 152.77 2.15 34 9 46 37 152.72 2.16 35 9 47 38 152.64 2.16 36 9 149 140 15.53 0.46 37 10 13 3 524.99 3.67 38 10 14 4 514.04 1.55 39 10 149 139 15.54 0.47 40 10 150 140 15.91 0.65 41 11 14 3 521.33 5.20 42 11 15 4 511.38 2.87 43 11 18 7 429.52 27.68 44 11 23 12 179.18 0.36 45 11 26 15 179.24 0.35 46 11 27 16 179.22 0.35 47 12 15 3 512.21 0.20 48 12 16 4 462.88 2.34 49 12 23 11 186.81 4.11 50 12 38 26 164.12 1.94 51 12 47 35 152.75 2.14 52 13 146 133 22.30 0.64 53 13 147 134 21.86 0.40 54 13 148 135 22.29 0.62 55 13 149 136 21.71 0.42 56 14 147 133 22.50 0.53 57 15 18 3 533.65 0.35 58 16 50 34 150.06 2.18 59 18 22 4 489.42 0.64 60 18 23 5 487.81 0.16 61 19 22 3 497.80 3.56 62 19 23 4 494.83 3.33 63 20 23 3 510.61 2.03 64 20 24 4 491.10 0.53 65 20 31 11 190.45 3.10 66 20 34 14 190.41 3.12 67 20 35 15 190.31 3.10 68 20 38 18 190.28 3.12 69 21 24 3 507.61 6.26 70 21 25 4 492.37 0.10 71 21 31 10 190.45 3.10 72 22 25 3 514.82 2.66 73 22 26 4 493.81 0.61 74 23 26 3 504.31 0.77 75 23 27 4 492.55 1.25 76 23 34 11 190.44 3.10 77 24 27 3 521.64 9.44 78 24 28 4 492.54 1.24 79 24 29 5 475.10 1.85 80 24 31 7 208.31 6.19 81 24 34 10 190.44 3.10 82 25 28 3 498.45 4.47 83 27 34 7 470.89 3.06 84 29 34 5 489.44 0.88 85 30 33 3 502.05 0.68 86 30 34 4 497.63 2.89 87 31 34 3 499.79 2.37 88 31 35 4 496.54 2.13 89 32 35 3 510.51 0.47 90 32 36 4 498.72 3.20 91 33 36 3 500.06 3.83 92 33 37 4 500.03 3.81 93 34 37 3 517.60 0.40 94 34 38 4 507.99 0.14 95 35 38 3 523.62 1.74 96 35 39 4 508.50 0.12 97 36 39 3 524.29 3.73 98 36 40 4 512.54 2.14 99 37 40 3 512.55 2.14 100 37 41 4 508.50 0.12 101 38 41 3 512.55 2.14 102 38 42 4 508.54 0.10 103 38 47 9 360.76 5.55 104 38 50 12 211.37 0.90 105 39 42 3 527.83 1.99 106 39 43 4 508.53 0.09 107 40 43 3 508.61 0.12 108 40 44 4 508.51 0.09 109 41 44 3 508.51 0.08 110 41 45 4 499.60 3.95 111 41 46 5 462.48 2.34 112 41 47 6 451.88 2.96 113 42 45 3 506.24 0.62 114 42 47 5 418.32 19.74 115 42 50 8 403.75 27.03 116 45 48 3 512.73 3.65 117 47 50 3 660.32 4.03 118 54 59 5 506.81 1.28 119 55 58 3 515.78 1.52 120 55 59 4 512.55 0.10 121 56 59 3 511.01 0.68 122 56 60 4 510.87 0.74 123 56 61 5 422.44 33.16 124 56 108 52 234.25 3.86 125 57 60 3 506.94 1.36 126 59 110 51 326.76 0.12 127 60 110 50 326.76 0.12 128 61 64 3 557.15 0.41 129 61 108 47 326.79 0.32 130 61 109 48 326.79 0.32 131 61 110 49 334.73 0.62 132 62 109 47 335.69 0.52 133 62 110 48 335.72 0.53 134 63 108 45 335.89 0.59 135 63 109 46 335.74 0.53 136 63 111 48 335.74 0.53 137 63 112 49 335.71 0.52 138 63 115 52 335.73 0.53 139 64 107 43 336.62 0.24 140 64 108 44 336.59 0.24 141 64 136 72 100.02 1.08 142 64 137 73 95.11 1.01 143 64 140 76 90.43 1.07 144 65 106 41 336.84 0.31 145 65 107 42 336.66 0.26 146 65 109 44 336.66 0.26 147 65 115 50 336.59 0.25 148 65 134 69 107.78 1.14 149 65 135 70 103.25 0.64 150 65 136 71 100.25 0.98 151 65 137 72 98.09 2.03 152 66 104 38 338.21 0.24 153 66 105 39 336.97 0.30 154 66 106 40 336.89 0.29 155 66 134 68 107.85 1.10 156 66 135 69 106.56 1.71 157 66 137 71 101.06 1.32 158 67 103 36 338.82 0.01 159 67 104 37 338.63 0.04 160 67 105 38 337.00 0.30 161 67 119 52 336.76 0.27 162 67 132 65 187.03 14.26 163 67 133 66 110.88 0.24 164 67 134 67 107.85 1.10 165 68 102 34 338.88 0.03 166 68 103 35 338.82 0.01 167 68 104 36 338.71 0.06 168 68 132 64 199.24 8.15 169 68 133 65 124.36 1.03 170 69 81 12 338.88 0.02 171 69 85 16 338.83 0.03 172 69 102 33 338.89 0.02 173 69 103 34 338.83 0.01 174 69 105 36 338.82 0.01 175 69 129 60 320.78 1.28 176 69 131 62 289.00 2.31 177 69 132 63 218.08 1.27 178 70 102 32 338.89 0.03 179 70 129 59 332.69 0.42 180 70 130 60 317.41 0.60 181 70 131 61 298.81 0.81 182 71 78 7 338.95 0.01 183 71 81 10 338.93 0.02 184 71 128 57 335.06 0.52 185 71 130 59 327.73 2.07 186 72 77 5 425.98 17.33 187 72 127 55 335.87 0.56 188 72 128 56 335.14 0.56 189 72 129 57 335.05 0.51 190 72 130 58 334.13 0.81 191 73 78 5 451.11 4.84 192 74 77 3 513.82 0.02 193 76 79 3 512.01 2.45 194 76 80 4 509.37 1.14 195 77 80 3 512.08 0.23 196 77 81 4 504.89 1.10 197 77 128 51 335.76 0.57 198 78 81 3 510.32 0.68 199 78 82 4 507.51 0.22 200 78 96 18 433.80 0.05 201 78 103 25 432.86 0.40 202 79 82 3 517.95 2.71 203 79 83 4 507.51 0.22 204 80 83 3 523.66 0.15 205 80 84 4 508.77 2.54 206 80 128 48 336.46 0.32 207 81 84 3 517.52 2.91 208 81 85 4 508.78 2.54 209 81 103 22 435.51 0.34 210 81 126 45 336.63 0.33 211 81 128 47 335.49 0.60 212 81 129 48 334.86 0.92 213 82 85 3 519.83 1.77 214 82 86 4 509.09 2.39 215 82 103 21 435.45 0.37 216 83 86 3 510.75 1.87 217 83 87 4 509.09 2.39 218 84 87 3 515.35 0.43 219 84 88 4 509.09 2.39 220 84 126 42 336.81 0.28 221 84 127 43 336.77 0.29 222 84 128 44 336.53 0.36 223 85 88 3 530.95 1.50 224 85 91 6 436.60 0.70 225 85 94 9 435.79 0.34 226 85 103 18 435.85 0.30 227 85 105 20 435.77 0.31 228 85 123 38 336.94 0.24 229 85 126 41 336.68 0.33 230 86 91 5 435.74 0.29 231 86 94 8 435.78 0.35 232 87 122 35 340.07 0.01 233 88 91 3 519.53 2.19 234 88 109 21 435.74 0.33 235 88 118 30 340.08 0.01 236 88 119 31 340.06 0.01 237 88 122 34 340.06 0.01 238 88 123 35 340.00 0.01 239 88 126 38 339.73 0.04 240 89 109 20 435.69 0.32 241 89 122 33 340.09 0.01 242 90 107 17 435.83 0.38 243 90 108 18 435.73 0.33 244 90 109 19 435.69 0.32 245 91 94 3 591.39 0.51 246 91 105 14 436.19 0.36 247 91 106 15 436.14 0.37 248 91 107 16 435.88 0.35 249 91 109 18 435.88 0.35 250 91 119 28 340.09 0.01 251 92 106 14 436.19 0.39 252 92 107 15 436.12 0.38 253 92 108 16 436.13 0.37 254 93 105 12 436.23 0.38 255 93 106 13 436.22 0.37 256 94 103 9 436.62 0.41 257 94 104 10 436.51 0.45 258 94 105 11 436.23 0.37 259 95 103 8 436.62 0.41 260 95 104 9 436.53 0.45 261 95 106 11 436.51 0.45 262 96 101 5 439.80 1.11 263 96 102 6 436.70 0.41 264 96 103 7 436.67 0.40 265 97 101 4 439.80 1.11 266 97 102 5 436.71 0.41 267 97 104 7 436.69 0.40 268 98 101 3 439.81 1.11 269 105 119 14 339.94 0.01 270 108 143 35 73.73 1.63 271 109 114 5 463.25 2.89 272 109 115 6 437.12 0.50 273 109 118 9 342.10 0.96 274 109 119 10 342.20 1.03 275 110 114 4 496.60 1.23 276 111 114 3 499.25 2.38 277 111 115 4 490.42 2.04 278 112 115 3 499.20 2.35 279 112 116 4 490.42 2.04 280 113 116 3 499.59 2.23 281 113 117 4 490.73 2.21 282 114 117 3 500.42 1.81 283 114 118 4 484.75 5.19 284 115 119 4 457.69 8.33 285 115 120 5 456.75 7.66 286 115 134 19 107.85 1.08 287 116 120 4 439.69 0.67 288 116 121 5 439.70 0.66 289 117 121 4 461.47 5.44 290 118 122 4 504.69 5.33 291 119 122 3 517.51 1.08 292 119 123 4 504.57 4.75 293 120 123 3 514.60 0.38 294 120 124 4 505.23 5.07 295 121 124 3 522.09 3.37 296 121 125 4 514.09 0.64 297 122 125 3 520.60 2.60 298 122 126 4 514.10 0.64 299 123 126 3 514.10 0.64 300 123 129 6 352.10 4.01 301 123 132 9 210.33 2.38 302 126 129 3 507.20 1.16 303 129 132 3 600.23 3.08 304 137 140 3 556.80 4.17 305 140 143 3 553.90 1.71 306 144 147 3 525.51 2.64 307 145 148 3 557.43 2.33 308 147 150 3 553.02 1.79